diff --git a/.github/workflows/local_modules.yml b/.github/workflows/local_modules.yml
index ba5a322283..838351536d 100644
--- a/.github/workflows/local_modules.yml
+++ b/.github/workflows/local_modules.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ['20.11.0-edge']
+        nxf_version: ['21.04.0']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
         profile: ['docker', 'singularity'] ## 'conda'
     env:
diff --git a/.gitignore b/.gitignore
index 7620ce70a0..09ece0f765 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,7 +4,6 @@ work/
 data/
 results/
 .DS_Store
-tests/
 testing/
 testing*
 *.pyc
diff --git a/.nf-core-lint.yml b/.nf-core-lint.yml
index 7e6a595c7e..f0a130b3ba 100644
--- a/.nf-core-lint.yml
+++ b/.nf-core-lint.yml
@@ -2,5 +2,7 @@ files_unchanged:
   - .github/ISSUE_TEMPLATE/bug_report.md
   - .github/ISSUE_TEMPLATE/feature_request.md
   - .github/PULL_REQUEST_TEMPLATE.md
+  - .gitignore
   - assets/nf-core-sarek_logo.png
   - docs/images/nf-core-sarek_logo.png
+  - lib/NfcoreSchema.groovy
diff --git a/assets/dummy_file.txt b/assets/dummy_file.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/bin/concatenateVCFs.sh b/bin/concatenateVCFs.sh
index 2c4d376a44..d1ea48cc8d 100755
--- a/bin/concatenateVCFs.sh
+++ b/bin/concatenateVCFs.sh
@@ -8,27 +8,27 @@ usage() { echo "Usage: $0 [-i genome_index_file] [-o output.file.no.gz.extension
 
 while [[ $# -gt 0 ]]
 do
-  key=$1
-  case $key in
+	key=$1
+	case $key in
 		-i)
 			genomeIndex=$2
 			shift # past argument
-	    shift # past value
+			shift # past value
 			;;
 		-c)
 			cpus=$2
 			shift # past argument
-	    shift # past value
+			shift # past value
 			;;
 		-o)
 			outputFile=$2
 			shift # past argument
-	    shift # past value
+			shift # past value
 			;;
 		-t)
 			targetBED=$2
 			shift # past argument
-	    shift # past value
+			shift # past value
 			;;
 		-n)
 			noInt=1
@@ -46,7 +46,7 @@ if [ -z ${cpus} ]; then echo "No CPUs defined: setting to 1"; cpus=1; fi
 if [ -z ${outputFile} ]; then echo "Missing output file name"; usage; fi
 
 
-if [ -z ${noInt+x} ] 
+if [ -z ${noInt+x} ]
 then
 	# First make a header from one of the VCF
 	# Remove interval information from the GATK command-line, but leave the rest
@@ -62,36 +62,36 @@ then
 	
 	# Concatenate VCFs in the correct order
 	(
-	  cat header
+		cat header
 	
-	  for chr in "${CONTIGS[@]}"; do
-	    # Skip if globbing would not match any file to avoid errors such as
-	    # "ls: cannot access chr3_*.vcf: No such file or directory" when chr3
-	    # was not processed.
-	    pattern="${chr}_*.vcf"
-	    if ! compgen -G "${pattern}" > /dev/null; then continue; fi
+		for chr in "${CONTIGS[@]}"; do
+			# Skip if globbing would not match any file to avoid errors such as
+			# "ls: cannot access chr3_*.vcf: No such file or directory" when chr3
+			# was not processed.
+			pattern="${chr}_*.vcf"
+			if ! compgen -G "${pattern}" > /dev/null; then continue; fi
 	
-	    # ls -v sorts by numeric value ("version"), which means that chr1_100_
-	    # is sorted *after* chr1_99_.
-	    for vcf in $(ls -v ${pattern}); do
-	      # Determine length of header.
-	      # The 'q' command makes sed exit when it sees the first non-header
-	      # line, which avoids reading in the entire file.
-	      L=$(sed -n '/^[^#]/q;p' ${vcf} | wc -l)
-	
-	      # Then print all non-header lines. Since tail is very fast (nearly as
-	      # fast as cat), this is way more efficient than using a single sed,
-	      # awk or grep command.
-	      tail -n +$((L+1)) ${vcf}
-	    done
-	  done
+			# ls -v sorts by numeric value ("version"), which means that chr1_100_
+			# is sorted *after* chr1_99_.
+			for vcf in $(ls -v ${pattern}); do
+				# Determine length of header.
+				# The 'q' command makes sed exit when it sees the first non-header
+				# line, which avoids reading in the entire file.
+				L=$(sed -n '/^[^#]/q;p' ${vcf} | wc -l)
+
+				# Then print all non-header lines. Since tail is very fast (nearly as
+				# fast as cat), this is way more efficient than using a single sed,
+				# awk or grep command.
+				tail -n +$((L+1)) ${vcf}
+			done
+		done
 	) | bgzip -@${cpus} > rawcalls.vcf.gz
 	tabix rawcalls.vcf.gz
 else
-        VCF=$(ls no_intervals*.vcf)
-        cp $VCF rawcalls.vcf 
-        bgzip -@${cpus} rawcalls.vcf
-        tabix rawcalls.vcf.gz
+	VCF=$(ls no_intervals*.vcf)
+	cp $VCF rawcalls.vcf
+	bgzip -@${cpus} rawcalls.vcf
+	tabix rawcalls.vcf.gz
 fi
 
 set +u
diff --git a/conf/genomes.config b/conf/genomes.config
index edbbfd868c..9e74db8dde 100644
--- a/conf/genomes.config
+++ b/conf/genomes.config
@@ -79,5 +79,15 @@ params {
     'custom' {
       fasta                   = null
     }
+    'small_hg38' {
+      dbsnp                   = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
+      fasta                   = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta"
+      fasta_fai               = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
+      germline_resource       = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
+      known_indels            = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
+      snpeff_db               = 'GRCh38.86'
+      species                 = 'homo_sapiens'
+      vep_cache_version       = '99'
+    }
   }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 800c7e1976..1e43a0b83b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -8,202 +8,212 @@ params {
     modules {
 // BUILD_INDICES
         'build_intervals' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'bwa_index' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'bwamem2_index' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'create_intervals_bed' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'dict' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'index_target_bed' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
-        'msisensor_scan' {
-            publish_dir      = "reference"
+        'msisensorpro_scan' {
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'samtools_faidx' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'tabix_dbsnp' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'tabix_germline_resource' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'tabix_known_indels' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
         'tabix_pon' {
-            publish_dir      = "reference"
+            publish_dir      = 'reference'
             publish_files    = false
         }
 // MAPPING
         'bwa_mem1_mem' {
-            args             = "-K 100000000 -M"
-            args2            = "sort"
+            args             = '-K 100000000 -M'
+            args2            = 'sort'
             publish_files    = false
         }
         'bwa_mem1_mem_tumor' {
-            args             = "-K 100000000 -M -B 3"
-            args2            = "sort"
+            args             = '-K 100000000 -M -B 3'
+            args2            = 'sort'
             publish_files    = false
         }
         'bwa_mem2_mem' {
-            args             = "-K 100000000 -M"
-            args2            = "sort"
+            args             = '-K 100000000 -M'
+            args2            = 'sort'
             publish_files    = false
         }
         'bwa_mem2_mem_tumor' {
-            args             = "-K 100000000 -M -B 3"
-            args2            = "sort"
+            args             = '-K 100000000 -M -B 3'
+            args2            = 'sort'
             publish_files    = false
         }
         'merge_bam_mapping' {
-            publish_by_id    = "true"
+            publish_by_meta  = true
             publish_files    = ['bam':'mapped']
-            publish_dir      = "preprocessing"
+            publish_dir      = 'preprocessing'
         }
         'qualimap_bamqc_mapping' {
-            publish_by_id    = "true"
-            publish_dir      = "reports/qualimap"
+            args             = '--paint-chromosome-limits --genome-gc-distr HUMAN -skip-duplicated --skip-dup-mode 0 -outformat HTML'
+            publish_by_meta  = true
+            publish_dir      = 'reports/qualimap'
         }
         'samtools_index_mapping' {
-            publish_by_id    = "true"
+            publish_by_meta  = true
             publish_files    = ['bai':'mapped']
-            publish_dir      = "preprocessing"
+            publish_dir      = 'preprocessing'
         }
         'samtools_stats_mapping' {
-            publish_by_id    = "true"
-            publish_dir      = "reports/samtools_stats"
+            publish_by_meta  = true
+            publish_dir      = 'reports/samtools_stats'
         }
 // MARKDUPLICATES
         'markduplicates' {
-            args             = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
-            suffix           = ".md"
-            publish_by_id    = "true"
-            publish_dir      = "preprocessing"
-            publish_files    = ['md.bam': 'markduplicates', 'md.bam.bai': 'markduplicates']
+            args             = 'REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT'
+            suffix           = '.md'
+            publish_by_meta  = true
+            publish_dir      = 'preprocessing'
+            publish_files    = ['bam': 'markduplicates', 'bai': 'markduplicates']
+        }
+        'markduplicatesspark' {
+            args             = '--remove-sequencing-duplicates false -VS LENIENT'
+            suffix           = '.md'
+            publish_by_meta  = true
+            publish_dir      = 'preprocessing'
+            publish_files    = ['bam': 'markduplicates', 'bai': 'markduplicates']
         }
 // PREPARE_RECALIBRATION
         'baserecalibrator' {
-            publish_by_id    = "true"
-            publish_dir      = "preprocessing"
-            publish_files    = ['recal.table':'markduplicates']
+            publish_by_meta  = true
+            publish_dir      = 'preprocessing'
+            publish_files    = ['recal.table': 'recal_table']
         }
         'gatherbqsrreports' {
-            publish_by_id    = "true"
-            publish_dir      = "preprocessing"
-            publish_files    = ['recal.table':'markduplicates']
+            publish_by_meta  = true
+            publish_dir      = 'preprocessing'
+            publish_files    = ['recal.table': 'recal_table']
         }
 // RECALIBRATE
         'applybqsr' {
-            suffix           = "recal"
-            publish_by_id    = "true"
-            publish_dir      = "preprocessing"
+            suffix           = '.recal'
+            publish_files    = false
         }
         'merge_bam_recalibrate' {
-            suffix           = ".recal"
-            publish_by_id    = "true"
+            suffix           = '.recal'
+            publish_by_meta  = true
             publish_files    = ['bam':'recalibrated']
-            publish_dir      = "preprocessing"
+            publish_dir      = 'preprocessing'
         }
         'qualimap_bamqc_recalibrate' {
-            publish_by_id    = "true"
-            publish_dir      = "reports/qualimap"
+            args             = '--paint-chromosome-limits --genome-gc-distr HUMAN -skip-duplicated --skip-dup-mode 0 -outformat HTML'
+            publish_by_meta  = true
+            publish_dir      = 'reports/qualimap'
         }
         'samtools_index_recalibrate' {
-            suffix           = "recal"
-            publish_by_id    = "true"
-            publish_dir      = "preprocessing"
+            suffix           = 'recal'
+            publish_by_meta  = true
+            publish_dir      = 'preprocessing'
             publish_files    = ['recal.bam':'recalibrated', 'recal.bam.bai':'recalibrated']
         }
         'samtools_stats_recalibrate' {
-            publish_by_id    = "true"
-            publish_dir      = "reports/samtools_stats"
+            publish_by_meta  = true
+            publish_dir      = 'reports/samtools_stats'
         }
 // GERMLINE_VARIANT_CALLING
         'haplotypecaller' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            args             = '-ERC GVCF'
+            suffix           = '.g'
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = false
         }
         'genotypegvcf' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = false
         }
         'concat_haplotypecaller' {
-            suffix           = "haplotypecaller"
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            suffix           = 'haplotypecaller'
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'haplotypecaller', 'vcf.gz.tbi':'haplotypecaller']
         }
         'concat_gvcf' {
-            suffix           = "haplotypecaller_gvcf"
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            suffix           = 'haplotypecaller_gvcf'
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'haplotypecaller_gvcf', 'vcf.gz.tbi':'haplotypecaller_gvcf']
         }
         'strelka_germline' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
         }
 // TUMOR_VARIANT_CALLING
 
 // PAIR_VARIANT_CALLING
         'manta_somatic' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'manta', 'vcf.gz.tbi':'manta']
         }
-        'msisensor_msi' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
-            publish_files    = ['list':'msisensor']
+        'msisensorpro_msi' {
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
+            publish_files    = ['list':'msisensorpro']
         }
         'strelka_somatic' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
         }
         'strelka_somatic_bp' {
-            publish_by_id    = "true"
-            publish_dir      = "variant_calling"
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
         }
 // QC_TRIM
         'fastqc' {
-            args             = "--quiet"
-            publish_by_id    = "true"
-            publish_dir      = "reports/fastqc"
+            args             = '--quiet'
+            publish_by_meta  = true
+            publish_dir      = 'reports/fastqc'
         }
         'trimgalore' {
-            args             = "--fastqc"
-            publish_by_id    = "true"
-            publish_dir      = "trimgalore"
+            args             = '--fastqc'
+            publish_by_meta  = true
+            publish_dir      = 'trimgalore'
         }
 // OTHERS
         'get_software_versions' {
-            publish_dir      = "pipeline_info"
+            publish_dir      = 'pipeline_info'
         }
     }
 }
diff --git a/conf/test.config b/conf/test.config
index 7ad28d55ec..d4f8912045 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test,<docker/singularity>
+ *   nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity>
  */
 
 params {
@@ -17,7 +17,7 @@ params {
   max_time = 48.h
 
   // Input data
-  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-normal-https.tsv'
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-manta-normal-https.csv'
 
   // Small reference genome
   igenomes_ignore = true
@@ -31,6 +31,61 @@ params {
   schema_ignore_params = 'genomes,input'
 }
 
+profiles {
+  annotation {
+    params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
+    params.genome              = 'WBcel235'
+    params.igenomes_ignore     = false
+  }
+  pair {
+    params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-manta-https.csv'
+  }
+  save_bam_mapped {
+    params.save_bam_mapped     = true
+  }
+  split_fastq {
+    params.split_fastq         = 500
+  }
+  targeted {
+    params.target_bed          = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/target.bed'
+    params.tools               = 'manta,strelka'
+  }
+  tool {
+    params.step                = 'variant_calling'
+    params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-recal-normal-https.csv'
+  }
+  tool_pair {
+    params.step                = 'variant_calling'
+    params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-recal-pair-https.csv'
+    }
+  trimming {
+    params.trim_fastq          = true
+    params.clip_r1             = 1
+    params.clip_r2             = 1
+    params.three_prime_clip_r1 = 1
+    params.three_prime_clip_r2 = 1
+  }
+  use_gatk_spark {
+    params.use_gatk_spark      = true
+  }
+  umi_quiaseq {
+    params.genome              = 'smallGRCh38'
+    params.genomes_base        = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/chr20_hg38'
+    params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-umi-qiaseq-https.csv'
+    params.umi                 = true
+    params.read_structure1     = "12M11S+T"
+    params.read_structure2     = "12M11S+T"
+  }
+  umi_tso {
+    genome                     = 'smallGRCh38'
+    genomes_base               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/chr20_hg38'
+    input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-umi-tso-https.csv'
+    umi                        = true
+    read_structure1            = "7M1S+T"
+    read_structure2            = "7M1S+T"
+  }
+}
+
 /*
  * TODO: uncomment when ready
   process {
diff --git a/conf/test_annotation.config b/conf/test_annotation.config
deleted file mode 100644
index bbcf38cb88..0000000000
--- a/conf/test_annotation.config
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_annotation
- */
-
-includeConfig 'test.config'
-
-params {
-  input             = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
-  genome            = 'WBcel235'
-  igenomes_ignore   = false
-}
\ No newline at end of file
diff --git a/conf/test_full.config b/conf/test_full.config
index 74b118ef36..2ef0836093 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -14,11 +14,7 @@ params {
   // Input data for full size test
   // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
   // TODO nf-core: Give any required params for the test so that command line flags are not needed
-  single_end = false
-  input_paths = [
-    ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
-    ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
-  ]
+
   // Ignore `--input` as otherwise the parameter validation will throw an error
-  schema_ignore_params = 'genomes,input_paths,input'
+  schema_ignore_params = 'genomes,input'
 }
diff --git a/conf/test_germline_variantcalling.config b/conf/test_germline_variantcalling.config
deleted file mode 100644
index 7cec01feca..0000000000
--- a/conf/test_germline_variantcalling.config
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_tool
- */
-
-includeConfig 'test.config'
-
-params {
-  // Input data
-  tools = 'haplotypecaller,strelka'
-}
\ No newline at end of file
diff --git a/conf/test_pair.config b/conf/test_pair.config
deleted file mode 100644
index 493b152c2b..0000000000
--- a/conf/test_pair.config
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_pair,<docker/singularity>
- */
-
-includeConfig 'test.config'
-
-params {
-  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv'
-}
\ No newline at end of file
diff --git a/conf/test_split_fastq.config b/conf/test_split_fastq.config
deleted file mode 100644
index d2e6595caf..0000000000
--- a/conf/test_split_fastq.config
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_split_fastq
- */
-
-includeConfig 'test.config'
-
-params {
-  split_fastq = 500
-}
diff --git a/conf/test_targeted.config b/conf/test_targeted.config
deleted file mode 100644
index 9d3b38307e..0000000000
--- a/conf/test_targeted.config
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_targeted
- */
-
-includeConfig 'test.config'
-
-params {
-  target_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/target.bed'
-  tools = 'manta,strelka'
-}
diff --git a/conf/test_tool.config b/conf/test_tool.config
deleted file mode 100644
index 3d9a934533..0000000000
--- a/conf/test_tool.config
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_tool
- */
-
-includeConfig 'test.config'
-
-params {
-  // Input data
-  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-recal-pair-https.tsv'
-  step = 'variantcalling'
-}
\ No newline at end of file
diff --git a/conf/test_trimming.config b/conf/test_trimming.config
deleted file mode 100644
index f9a4af2da2..0000000000
--- a/conf/test_trimming.config
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_trimming
- */
-
-includeConfig 'test.config'
-
-params {
-  trim_fastq = true
-  clip_r1 = 1
-  clip_r2 = 1
-  three_prime_clip_r1 = 1
-  three_prime_clip_r2 = 1
-}
\ No newline at end of file
diff --git a/conf/test_umi_qiaseq.config b/conf/test_umi_qiaseq.config
deleted file mode 100644
index fd4d047a36..0000000000
--- a/conf/test_umi_qiaseq.config
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_umi_qiaseq
- */
-
-includeConfig 'test.config'
-
-params {
-  genome = 'smallGRCh38'
-  genomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/chr20_hg38'
-  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-umi-qiaseq-https.tsv'
-  umi = true
-  read_structure1 = "12M11S+T"
-  read_structure2 = "12M11S+T"
-}
\ No newline at end of file
diff --git a/conf/test_umi_tso.config b/conf/test_umi_tso.config
deleted file mode 100644
index d87e5e47cc..0000000000
--- a/conf/test_umi_tso.config
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_umi_tso
- */
-
-includeConfig 'test.config'
-
-params {
-  genome = 'smallGRCh38'
-  genomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/chr20_hg38'
-  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-umi-tso-https.tsv'
-  umi = true
-  read_structure1 = "7M1S+T"
-  read_structure2 = "7M1S+T"
-}
\ No newline at end of file
diff --git a/conf/test_use_gatk_spark.config b/conf/test_use_gatk_spark.config
deleted file mode 100644
index 7668782c33..0000000000
--- a/conf/test_use_gatk_spark.config
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/sarek -profile test_use_gatk_spark
- */
-
-includeConfig 'test.config'
-
-params {
-  use_gatk_spark = true
-}
\ No newline at end of file
diff --git a/lib/Checks.groovy b/lib/Checks.groovy
deleted file mode 100644
index 63c9cf5cfc..0000000000
--- a/lib/Checks.groovy
+++ /dev/null
@@ -1,102 +0,0 @@
-import org.yaml.snakeyaml.Yaml
-
-/*
- * This file holds several functions used to perform standard checks for the nf-core pipeline template.
- */
-
-class Checks {
-
-    static void check_conda_channels(log) {
-        Yaml parser = new Yaml()
-        def channels = []
-        try {
-            def config = parser.load("conda config --show channels".execute().text)
-            channels = config.channels
-        } catch(NullPointerException | IOException e) {
-            log.warn "Could not verify conda channel configuration."
-            return
-        }
-
-        // Check that all channels are present
-        def required_channels = ['conda-forge', 'bioconda', 'defaults']
-        def conda_check_failed = !required_channels.every { ch -> ch in channels }
-
-        // Check that they are in the right order
-        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
-        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
-
-        if (conda_check_failed) {
-            log.warn "=============================================================================\n" +
-                     "  There is a problem with your Conda configuration!\n\n" + 
-                     "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                     "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
-                     "  NB: The order of the channels matters!\n" +
-                     "==================================================================================="
-        }
-    }
-
-    static void aws_batch(workflow, params) {
-        if (workflow.profile.contains('awsbatch')) {
-            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-            // Check outdir paths to be S3 buckets if running on AWSBatch
-            // related: https://github.com/nextflow-io/nextflow/issues/813
-            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
-            // Prevent trace files to be stored on S3 since S3 does not support rolling files.
-            assert !params.tracedir.startsWith('s3:')    :  "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
-        }
-    }
-
-    static void hostname(workflow, params, log) {
-        Map colors = Headers.log_colours(params.monochrome_logs)
-        if (params.hostnames) {
-            def hostname = "hostname".execute().text.trim()
-            params.hostnames.each { prof, hnames ->
-                hnames.each { hname ->
-                    if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
-                        log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
-                                  "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
-                                  "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
-                                  "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
-                                  "=${colors.yellow}====================================================${colors.reset}="
-                    }
-                }
-            }
-        }
-    }
-
-    // Citation string
-    private static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-               "* The pipeline\n" + 
-               "  https://doi.org/10.12688/f1000research.16665.2\n" +
-               "  https://doi.org/10.5281/zenodo.4468605\n\n" +
-               "* The nf-core framework\n" +
-               "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-               "* Software dependencies\n" +
-               "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-    // Exit pipeline if incorrect --genome key provided
-    static void genome_exists(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            log.error "=============================================================================\n" +
-                      "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                      "  Currently, the available genome keys are:\n" +
-                      "  ${params.genomes.keySet().join(", ")}\n" +
-                      "============================================================================="
-            System.exit(0)
-        }
-    }
-
-    // Get attribute from genome config file e.g. fasta
-    static String get_genome_attribute(params, attribute) {
-        def val = ''
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                val = params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return val
-    }
-
-}
diff --git a/lib/Completion.groovy b/lib/Completion.groovy
deleted file mode 100644
index 5a933eb9a5..0000000000
--- a/lib/Completion.groovy
+++ /dev/null
@@ -1,128 +0,0 @@
-/*
- * Functions to be run on completion of pipeline
- */
-
-class Completion {
-    static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
-
-        // Set up the e-mail variables
-        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-        if (!workflow.success) {
-            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
-        }
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-        
-        def misc_fields = [:]
-        misc_fields['Date Started']              = workflow.start
-        misc_fields['Date Completed']            = workflow.complete
-        misc_fields['Pipeline script file path'] = workflow.scriptFile
-        misc_fields['Pipeline script hash ID']   = workflow.scriptId
-        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-        misc_fields['Nextflow Version']           = workflow.nextflow.version
-        misc_fields['Nextflow Build']             = workflow.nextflow.build
-        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-        def email_fields = [:]
-        email_fields['version']             = workflow.manifest.version
-        email_fields['runName']             = workflow.runName
-        email_fields['success']             = workflow.success
-        email_fields['dateComplete']        = workflow.complete
-        email_fields['duration']            = workflow.duration
-        email_fields['exitStatus']          = workflow.exitStatus
-        email_fields['errorMessage']        = (workflow.errorMessage ?: 'None')
-        email_fields['errorReport']         = (workflow.errorReport ?: 'None')
-        email_fields['commandLine']         = workflow.commandLine
-        email_fields['projectDir']          = workflow.projectDir
-        email_fields['summary']             = summary << misc_fields
-        
-        // On success try attach the multiqc report
-        def mqc_report = null
-        try {
-            if (workflow.success && !params.skip_multiqc) {
-                mqc_report = multiqc_report.getVal()
-                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                    if (mqc_report.size() > 1) {
-                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                    }
-                    mqc_report = mqc_report[0]
-                }
-            }
-        } catch (all) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-        }
-
-        // Check if we are only sending emails on failure
-        def email_address = params.email
-        if (!params.email && params.email_on_fail && !workflow.success) {
-            email_address = params.email_on_fail
-        }
-
-        // Render the TXT template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        def tf           = new File("$projectDir/assets/email_template.txt")
-        def txt_template = engine.createTemplate(tf).make(email_fields)
-        def email_txt    = txt_template.toString()
-
-        // Render the HTML template
-        def hf            = new File("$projectDir/assets/email_template.html")
-        def html_template = engine.createTemplate(hf).make(email_fields)
-        def email_html    = html_template.toString()
-
-        // Render the sendmail template
-        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit 
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize:  max_multiqc_email_size.toBytes()]
-        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
-        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-        def sendmail_html          = sendmail_template.toString()
-
-        // Send the HTML e-mail
-        Map colors = Headers.log_colours(params.monochrome_logs)
-        if (email_address) {
-            try {
-                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-                // Try to send HTML e-mail using sendmail
-                [ 'sendmail', '-t' ].execute() << sendmail_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-            } catch (all) {
-                // Catch failures and try with plaintext
-                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
-                    mail_cmd += [ '-A', mqc_report ]
-                }
-                mail_cmd.execute() << email_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-            }
-        }
-
-        // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
-        output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
-        output_tf.withWriter { w -> w << email_txt }
-    }
-
-    static void summary(workflow, params, log) {
-        Map colors = Headers.log_colours(params.monochrome_logs)
-
-        if (workflow.success) {
-            if (workflow.stats.ignoredCount == 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-            } else {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
-            }
-        } else {
-            Checks.hostname(workflow, params, log)
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
-        }
-    }
-}
diff --git a/lib/Headers.groovy b/lib/Headers.groovy
deleted file mode 100644
index 9b066b42fe..0000000000
--- a/lib/Headers.groovy
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * This file holds several functions used to render the nf-core ANSI header.
- */
-
-class Headers {
-
-    private static Map log_colours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
-        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
-        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']      = monochrome_logs ? '' :  "\033[0;33m"
-        colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
-        colorcodes['red']         = monochrome_logs ? '' : "\033[1;91m"
-        return colorcodes
-    }
-
-    static String dashed_line(monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    static String nf_core(workflow, monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        String.format(
-            """\n
-            ${dashed_line(monochrome_logs)}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
-                  ${colors.white}____${colors.reset}
-                ${colors.white}.´ _  `.${colors.reset}
-               ${colors.white}/  ${colors.green}|\\${colors.reset}`-_ \\${colors.reset}     ${colors.blue} __        __   ___     ${colors.reset}
-              ${colors.white}|   ${colors.green}| \\${colors.reset}  `-|${colors.reset}    ${colors.blue}|__`  /\\  |__) |__  |__/${colors.reset}
-               ${colors.white}\\ ${colors.green}|   \\${colors.reset}  /${colors.reset}     ${colors.blue}.__| /¯¯\\ |  \\ |___ |  \\${colors.reset}
-                ${colors.white}`${colors.green}|${colors.reset}____${colors.green}\\${colors.reset}´${colors.reset}
-
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
-            ${dashed_line(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index 52ee730432..16986434f7 100644
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -1,6 +1,6 @@
-/*
- * This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
- */
+//
+// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
+//
 
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
@@ -13,16 +13,23 @@ import groovy.json.JsonBuilder
 
 class NfcoreSchema {
 
-    /*
-    * Function to loop over all parameters defined in schema and check
-    * whether the given paremeters adhere to the specificiations
-    */
+    //
+    // Resolve Schema path relative to main workflow directory
+    //
+    public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
+        return "${workflow.projectDir}/${schema_filename}"
+    }
+
+    //
+    // Function to loop over all parameters defined in schema and check
+    // whether the given parameters adhere to the specifications
+    //
     /* groovylint-disable-next-line UnusedPrivateMethodParameter */
-    private static void validateParameters(params, jsonSchema, log) {
+    public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
         def has_error = false
         //=====================================================================//
         // Check for nextflow core params and unexpected params
-        def json = new File(jsonSchema).text
+        def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
         def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
         def nf_params = [
             // Options for base `nextflow` command
@@ -125,36 +132,36 @@ class NfcoreSchema {
 
         //=====================================================================//
         // Validate parameters against the schema
-        InputStream inputStream = new File(jsonSchema).newInputStream()
-        JSONObject rawSchema = new JSONObject(new JSONTokener(inputStream))
+        InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
+        JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
 
         // Remove anything that's in params.schema_ignore_params
-        rawSchema = removeIgnoredParams(rawSchema, params)
+        raw_schema = removeIgnoredParams(raw_schema, params)
 
-        Schema schema = SchemaLoader.load(rawSchema)
+        Schema schema = SchemaLoader.load(raw_schema)
 
         // Clean the parameters
         def cleanedParams = cleanParameters(params)
 
         // Convert to JSONObject
         def jsonParams = new JsonBuilder(cleanedParams)
-        JSONObject paramsJSON = new JSONObject(jsonParams.toString())
+        JSONObject params_json = new JSONObject(jsonParams.toString())
 
         // Validate
         try {
-            schema.validate(paramsJSON)
+            schema.validate(params_json)
         } catch (ValidationException e) {
             println ''
             log.error 'ERROR: Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
-            printExceptions(exceptionJSON, paramsJSON, log)
+            printExceptions(exceptionJSON, params_json, log)
             println ''
             has_error = true
         }
 
         // Check for unexpected parameters
         if (unexpectedParams.size() > 0) {
-            Map colors = log_colours(params.monochrome_logs)
+            Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
             println ''
             def warn_msg = 'Found unexpected parameters:'
             for (unexpectedParam in unexpectedParams) {
@@ -170,266 +177,17 @@ class NfcoreSchema {
         }
     }
 
-    // Loop over nested exceptions and print the causingException
-    private static void printExceptions(exJSON, paramsJSON, log) {
-        def causingExceptions = exJSON['causingExceptions']
-        if (causingExceptions.length() == 0) {
-            def m = exJSON['message'] =~ /required key \[([^\]]+)\] not found/
-            // Missing required param
-            if (m.matches()) {
-                log.error "* Missing required parameter: --${m[0][1]}"
-            }
-            // Other base-level error
-            else if (exJSON['pointerToViolation'] == '#') {
-                log.error "* ${exJSON['message']}"
-            }
-            // Error with specific param
-            else {
-                def param = exJSON['pointerToViolation'] - ~/^#\//
-                def param_val = paramsJSON[param].toString()
-                log.error "* --${param}: ${exJSON['message']} (${param_val})"
-            }
-        }
-        for (ex in causingExceptions) {
-            printExceptions(ex, paramsJSON, log)
-        }
-    }
-
-    // Remove an element from a JSONArray
-    private static JSONArray removeElement(jsonArray, element){
-        def list = []
-        int len = jsonArray.length()
-        for (int i=0;i<len;i++){
-            list.add(jsonArray.get(i).toString())
-        }
-        list.remove(element)
-        JSONArray jsArray = new JSONArray(list)
-        return jsArray
-    }
-
-    private static JSONObject removeIgnoredParams(rawSchema, params){
-        // Remove anything that's in params.schema_ignore_params
-        params.schema_ignore_params.split(',').each{ ignore_param ->
-            if(rawSchema.keySet().contains('definitions')){
-                rawSchema.definitions.each { definition ->
-                    for (key in definition.keySet()){
-                        if (definition[key].get("properties").keySet().contains(ignore_param)){
-                            // Remove the param to ignore
-                            definition[key].get("properties").remove(ignore_param)
-                            // If the param was required, change this
-                            if (definition[key].has("required")) {
-                                def cleaned_required = removeElement(definition[key].required, ignore_param)
-                                definition[key].put("required", cleaned_required)
-                            }
-                        }
-                    }
-                }
-            }
-            if(rawSchema.keySet().contains('properties') && rawSchema.get('properties').keySet().contains(ignore_param)) {
-                rawSchema.get("properties").remove(ignore_param)
-            }
-            if(rawSchema.keySet().contains('required') && rawSchema.required.contains(ignore_param)) {
-                def cleaned_required = removeElement(rawSchema.required, ignore_param)
-                rawSchema.put("required", cleaned_required)
-            }
-        }
-        return rawSchema
-    }
-
-    private static Map cleanParameters(params) {
-        def new_params = params.getClass().newInstance(params)
-        for (p in params) {
-            // remove anything evaluating to false
-            if (!p['value']) {
-                new_params.remove(p.key)
-            }
-            // Cast MemoryUnit to String
-            if (p['value'].getClass() == nextflow.util.MemoryUnit) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-            // Cast Duration to String
-            if (p['value'].getClass() == nextflow.util.Duration) {
-                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
-            }
-            // Cast LinkedHashMap to String
-            if (p['value'].getClass() == LinkedHashMap) {
-                new_params.replace(p.key, p['value'].toString())
-            }
-        }
-        return new_params
-    }
-
-     /*
-     * This method tries to read a JSON params file
-     */
-    private static LinkedHashMap params_load(String json_schema) {
-        def params_map = new LinkedHashMap()
-        try {
-            params_map = params_read(json_schema)
-        } catch (Exception e) {
-            println "Could not read parameters settings from JSON. $e"
-            params_map = new LinkedHashMap()
-        }
-        return params_map
-    }
-
-    private static Map log_colours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // Reset / Meta
-        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
-        colorcodes['bold']        = monochrome_logs ? '' : "\033[1m"
-        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
-        colorcodes['underlined']  = monochrome_logs ? '' : "\033[4m"
-        colorcodes['blink']       = monochrome_logs ? '' : "\033[5m"
-        colorcodes['reverse']     = monochrome_logs ? '' : "\033[7m"
-        colorcodes['hidden']      = monochrome_logs ? '' : "\033[8m"
-
-        // Regular Colors
-        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['red']         = monochrome_logs ? '' : "\033[0;31m"
-        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']      = monochrome_logs ? '' : "\033[0;33m"
-        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
-
-        // Bold
-        colorcodes['bblack']      = monochrome_logs ? '' : "\033[1;30m"
-        colorcodes['bred']        = monochrome_logs ? '' : "\033[1;31m"
-        colorcodes['bgreen']      = monochrome_logs ? '' : "\033[1;32m"
-        colorcodes['byellow']     = monochrome_logs ? '' : "\033[1;33m"
-        colorcodes['bblue']       = monochrome_logs ? '' : "\033[1;34m"
-        colorcodes['bpurple']     = monochrome_logs ? '' : "\033[1;35m"
-        colorcodes['bcyan']       = monochrome_logs ? '' : "\033[1;36m"
-        colorcodes['bwhite']      = monochrome_logs ? '' : "\033[1;37m"
-
-        // Underline
-        colorcodes['ublack']      = monochrome_logs ? '' : "\033[4;30m"
-        colorcodes['ured']        = monochrome_logs ? '' : "\033[4;31m"
-        colorcodes['ugreen']      = monochrome_logs ? '' : "\033[4;32m"
-        colorcodes['uyellow']     = monochrome_logs ? '' : "\033[4;33m"
-        colorcodes['ublue']       = monochrome_logs ? '' : "\033[4;34m"
-        colorcodes['upurple']     = monochrome_logs ? '' : "\033[4;35m"
-        colorcodes['ucyan']       = monochrome_logs ? '' : "\033[4;36m"
-        colorcodes['uwhite']      = monochrome_logs ? '' : "\033[4;37m"
-
-        // High Intensity
-        colorcodes['iblack']      = monochrome_logs ? '' : "\033[0;90m"
-        colorcodes['ired']        = monochrome_logs ? '' : "\033[0;91m"
-        colorcodes['igreen']      = monochrome_logs ? '' : "\033[0;92m"
-        colorcodes['iyellow']     = monochrome_logs ? '' : "\033[0;93m"
-        colorcodes['iblue']       = monochrome_logs ? '' : "\033[0;94m"
-        colorcodes['ipurple']     = monochrome_logs ? '' : "\033[0;95m"
-        colorcodes['icyan']       = monochrome_logs ? '' : "\033[0;96m"
-        colorcodes['iwhite']      = monochrome_logs ? '' : "\033[0;97m"
-
-        // Bold High Intensity
-        colorcodes['biblack']     = monochrome_logs ? '' : "\033[1;90m"
-        colorcodes['bired']       = monochrome_logs ? '' : "\033[1;91m"
-        colorcodes['bigreen']     = monochrome_logs ? '' : "\033[1;92m"
-        colorcodes['biyellow']    = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['biblue']      = monochrome_logs ? '' : "\033[1;94m"
-        colorcodes['bipurple']    = monochrome_logs ? '' : "\033[1;95m"
-        colorcodes['bicyan']      = monochrome_logs ? '' : "\033[1;96m"
-        colorcodes['biwhite']     = monochrome_logs ? '' : "\033[1;97m"
-
-        return colorcodes
-    }
-
-    static String dashed_line(monochrome_logs) {
-        Map colors = log_colours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    /*
-    Method to actually read in JSON file using Groovy.
-    Group (as Key), values are all parameters
-        - Parameter1 as Key, Description as Value
-        - Parameter2 as Key, Description as Value
-        ....
-    Group
-        -
-    */
-    private static LinkedHashMap params_read(String json_schema) throws Exception {
-        def json = new File(json_schema).text
-        def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
-        def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
-        /* Tree looks like this in nf-core schema
-         * definitions <- this is what the first get('definitions') gets us
-             group 1
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-                   parameter 2
-                     type
-                     description
-             group 2
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-         * properties <- parameters can also be ungrouped, outside of definitions
-            parameter 1
-             type
-             description
-        */
-
-        // Grouped params
-        def params_map = new LinkedHashMap()
-        schema_definitions.each { key, val ->
-            def Map group = schema_definitions."$key".properties // Gets the property object of the group
-            def title = schema_definitions."$key".title
-            def sub_params = new LinkedHashMap()
-            group.each { innerkey, value ->
-                sub_params.put(innerkey, value)
-            }
-            params_map.put(title, sub_params)
-        }
-
-        // Ungrouped params
-        def ungrouped_params = new LinkedHashMap()
-        schema_properties.each { innerkey, value ->
-            ungrouped_params.put(innerkey, value)
-        }
-        params_map.put("Other parameters", ungrouped_params)
-
-        return params_map
-    }
-
-    /*
-     * Get maximum number of characters across all parameter names
-     */
-    private static Integer params_max_chars(params_map) {
-        Integer max_chars = 0
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (param.size() > max_chars) {
-                    max_chars = param.size()
-                }
-            }
-        }
-        return max_chars
-    }
-
-    /*
-     * Beautify parameters for --help
-     */
-    private static String params_help(workflow, params, json_schema, command) {
-        Map colors = log_colours(params.monochrome_logs)
+    //
+    // Beautify parameters for --help
+    //
+    public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
+        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
         Integer num_hidden = 0
         String output  = ''
         output        += 'Typical pipeline command:\n\n'
         output        += "  ${colors.cyan}${command}${colors.reset}\n\n"
-        Map params_map = params_load(json_schema)
-        Integer max_chars  = params_max_chars(params_map) + 1
+        Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
+        Integer max_chars  = paramsMaxChars(params_map) + 1
         Integer desc_indent = max_chars + 14
         Integer dec_linewidth = 160 - desc_indent
         for (group in params_map.keySet()) {
@@ -469,18 +227,17 @@ class NfcoreSchema {
                 output += group_output
             }
         }
-        output += dashed_line(params.monochrome_logs)
         if (num_hidden > 0){
-            output += colors.dim + "\n Hiding $num_hidden params, use --show_hidden_params to show.\n" + colors.reset
-            output += dashed_line(params.monochrome_logs)
+            output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
         }
+        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
         return output
     }
 
-    /*
-     * Groovy Map summarising parameters/workflow options used by the pipeline
-     */
-    private static LinkedHashMap params_summary_map(workflow, params, json_schema) {
+    //
+    // Groovy Map summarising parameters/workflow options used by the pipeline
+    //
+    public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
         // Get a selection of core Nextflow workflow options
         def Map workflow_summary = [:]
         if (workflow.revision) {
@@ -503,7 +260,7 @@ class NfcoreSchema {
         // Get pipeline parameters defined in JSON Schema
         def Map params_summary = [:]
         def blacklist  = ['hostnames']
-        def params_map = params_load(json_schema)
+        def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
         for (group in params_map.keySet()) {
             def sub_params = new LinkedHashMap()
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
@@ -546,14 +303,14 @@ class NfcoreSchema {
         return [ 'Core Nextflow options' : workflow_summary ] << params_summary
     }
 
-    /*
-     * Beautify parameters for summary and return as string
-     */
-    private static String params_summary_log(workflow, params, json_schema) {
-        Map colors = log_colours(params.monochrome_logs)
+    //
+    // Beautify parameters for summary and return as string
+    //
+    public static String paramsSummaryLog(workflow, params) {
+        Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
         String output  = ''
-        def params_map = params_summary_map(workflow, params, json_schema)
-        def max_chars  = params_max_chars(params_map)
+        def params_map = paramsSummaryMap(workflow, params)
+        def max_chars  = paramsMaxChars(params_map)
         for (group in params_map.keySet()) {
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
             if (group_params) {
@@ -564,10 +321,196 @@ class NfcoreSchema {
                 output += '\n'
             }
         }
-        output += dashed_line(params.monochrome_logs)
-        output += colors.dim + "\n Only displaying parameters that differ from defaults.\n" + colors.reset
-        output += dashed_line(params.monochrome_logs)
+        output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
+        output += NfcoreTemplate.dashedLine(params.monochrome_logs)
         return output
     }
 
+    //
+    // Loop over nested exceptions and print the causingException
+    //
+    private static void printExceptions(ex_json, params_json, log) {
+        def causingExceptions = ex_json['causingExceptions']
+        if (causingExceptions.length() == 0) {
+            def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
+            // Missing required param
+            if (m.matches()) {
+                log.error "* Missing required parameter: --${m[0][1]}"
+            }
+            // Other base-level error
+            else if (ex_json['pointerToViolation'] == '#') {
+                log.error "* ${ex_json['message']}"
+            }
+            // Error with specific param
+            else {
+                def param = ex_json['pointerToViolation'] - ~/^#\//
+                def param_val = params_json[param].toString()
+                log.error "* --${param}: ${ex_json['message']} (${param_val})"
+            }
+        }
+        for (ex in causingExceptions) {
+            printExceptions(ex, params_json, log)
+        }
+    }
+
+    //
+    // Remove an element from a JSONArray
+    //
+    private static JSONArray removeElement(json_array, element) {
+        def list = []
+        int len = json_array.length()
+        for (int i=0;i<len;i++){
+            list.add(json_array.get(i).toString())
+        }
+        list.remove(element)
+        JSONArray jsArray = new JSONArray(list)
+        return jsArray
+    }
+
+    //
+    // Remove ignored parameters
+    //
+    private static JSONObject removeIgnoredParams(raw_schema, params) {
+        // Remove anything that's in params.schema_ignore_params
+        params.schema_ignore_params.split(',').each{ ignore_param ->
+            if(raw_schema.keySet().contains('definitions')){
+                raw_schema.definitions.each { definition ->
+                    for (key in definition.keySet()){
+                        if (definition[key].get("properties").keySet().contains(ignore_param)){
+                            // Remove the param to ignore
+                            definition[key].get("properties").remove(ignore_param)
+                            // If the param was required, change this
+                            if (definition[key].has("required")) {
+                                def cleaned_required = removeElement(definition[key].required, ignore_param)
+                                definition[key].put("required", cleaned_required)
+                            }
+                        }
+                    }
+                }
+            }
+            if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
+                raw_schema.get("properties").remove(ignore_param)
+            }
+            if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
+                def cleaned_required = removeElement(raw_schema.required, ignore_param)
+                raw_schema.put("required", cleaned_required)
+            }
+        }
+        return raw_schema
+    }
+
+    //
+    // Clean and check parameters relative to Nextflow native classes
+    //
+    private static Map cleanParameters(params) {
+        def new_params = params.getClass().newInstance(params)
+        for (p in params) {
+            // remove anything evaluating to false
+            if (!p['value']) {
+                new_params.remove(p.key)
+            }
+            // Cast MemoryUnit to String
+            if (p['value'].getClass() == nextflow.util.MemoryUnit) {
+                new_params.replace(p.key, p['value'].toString())
+            }
+            // Cast Duration to String
+            if (p['value'].getClass() == nextflow.util.Duration) {
+                new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
+            }
+            // Cast LinkedHashMap to String
+            if (p['value'].getClass() == LinkedHashMap) {
+                new_params.replace(p.key, p['value'].toString())
+            }
+        }
+        return new_params
+    }
+
+    //
+    // This function tries to read a JSON params file
+    //
+    private static LinkedHashMap paramsLoad(String json_schema) {
+        def params_map = new LinkedHashMap()
+        try {
+            params_map = paramsRead(json_schema)
+        } catch (Exception e) {
+            println "Could not read parameters settings from JSON. $e"
+            params_map = new LinkedHashMap()
+        }
+        return params_map
+    }
+
+    //
+    // Method to actually read in JSON file using Groovy.
+    // Group (as Key), values are all parameters
+    //    - Parameter1 as Key, Description as Value
+    //    - Parameter2 as Key, Description as Value
+    //    ....
+    // Group
+    //    -
+    private static LinkedHashMap paramsRead(String json_schema) throws Exception {
+        def json = new File(json_schema).text
+        def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
+        def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
+        /* Tree looks like this in nf-core schema
+        * definitions <- this is what the first get('definitions') gets us
+                group 1
+                    title
+                    description
+                        properties
+                        parameter 1
+                            type
+                            description
+                        parameter 2
+                            type
+                            description
+                group 2
+                    title
+                    description
+                        properties
+                        parameter 1
+                            type
+                            description
+        * properties <- parameters can also be ungrouped, outside of definitions
+                parameter 1
+                    type
+                    description
+        */
+
+        // Grouped params
+        def params_map = new LinkedHashMap()
+        schema_definitions.each { key, val ->
+            def Map group = schema_definitions."$key".properties // Gets the property object of the group
+            def title = schema_definitions."$key".title
+            def sub_params = new LinkedHashMap()
+            group.each { innerkey, value ->
+                sub_params.put(innerkey, value)
+            }
+            params_map.put(title, sub_params)
+        }
+
+        // Ungrouped params
+        def ungrouped_params = new LinkedHashMap()
+        schema_properties.each { innerkey, value ->
+            ungrouped_params.put(innerkey, value)
+        }
+        params_map.put("Other parameters", ungrouped_params)
+
+        return params_map
+    }
+
+    //
+    // Get maximum number of characters across all parameter names
+    //
+    private static Integer paramsMaxChars(params_map) {
+        Integer max_chars = 0
+        for (group in params_map.keySet()) {
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            for (param in group_params.keySet()) {
+                if (param.size() > max_chars) {
+                    max_chars = param.size()
+                }
+            }
+        }
+        return max_chars
+    }
 }
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
new file mode 100644
index 0000000000..e1e05e8520
--- /dev/null
+++ b/lib/NfcoreTemplate.groovy
@@ -0,0 +1,274 @@
+//
+// This file holds several functions used within the nf-core pipeline template.
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class NfcoreTemplate {
+
+    //
+    // Check AWS Batch related parameters have been specified correctly
+    //
+    public static void awsBatch(workflow, params) {
+        if (workflow.profile.contains('awsbatch')) {
+            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
+            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+            // Check outdir paths to be S3 buckets if running on AWSBatch
+            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+        }
+    }
+
+    //
+    // Check params.hostnames
+    //
+    public static void hostName(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        if (params.hostnames) {
+            def hostname = "hostname".execute().text.trim()
+            params.hostnames.each { prof, hnames ->
+                hnames.each { hname ->
+                    if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+                        log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+                            "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+                            "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+                            "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+                            "=${colors.yellow}====================================================${colors.reset}="
+                    }
+                }
+            }
+        }
+    }
+
+    //
+    // Construct and send completion email
+    //
+    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
+
+        // Set up the e-mail variables
+        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+        if (!workflow.success) {
+            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        }
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['Date Started']              = workflow.start
+        misc_fields['Date Completed']            = workflow.complete
+        misc_fields['Pipeline script file path'] = workflow.scriptFile
+        misc_fields['Pipeline script hash ID']   = workflow.scriptId
+        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+        misc_fields['Nextflow Version']           = workflow.nextflow.version
+        misc_fields['Nextflow Build']             = workflow.nextflow.build
+        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+        def email_fields = [:]
+        email_fields['version']             = workflow.manifest.version
+        email_fields['runName']             = workflow.runName
+        email_fields['success']             = workflow.success
+        email_fields['dateComplete']        = workflow.complete
+        email_fields['duration']            = workflow.duration
+        email_fields['exitStatus']          = workflow.exitStatus
+        email_fields['errorMessage']        = (workflow.errorMessage ?: 'None')
+        email_fields['errorReport']         = (workflow.errorReport ?: 'None')
+        email_fields['commandLine']         = workflow.commandLine
+        email_fields['projectDir']          = workflow.projectDir
+        email_fields['summary']             = summary << misc_fields
+
+        // On success try attach the multiqc report
+        def mqc_report = null
+        try {
+            if (workflow.success && !params.skip_multiqc) {
+                mqc_report = multiqc_report.getVal()
+                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                    if (mqc_report.size() > 1) {
+                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    }
+                    mqc_report = mqc_report[0]
+                }
+            }
+        } catch (all) {
+            if (multiqc_report) {
+                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            }
+        }
+
+        // Check if we are only sending emails on failure
+        def email_address = params.email
+        if (!params.email && params.email_on_fail && !workflow.success) {
+            email_address = params.email_on_fail
+        }
+
+        // Render the TXT template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def tf           = new File("$projectDir/assets/email_template.txt")
+        def txt_template = engine.createTemplate(tf).make(email_fields)
+        def email_txt    = txt_template.toString()
+
+        // Render the HTML template
+        def hf            = new File("$projectDir/assets/email_template.html")
+        def html_template = engine.createTemplate(hf).make(email_fields)
+        def email_html    = html_template.toString()
+
+        // Render the sendmail template
+        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize:  max_multiqc_email_size.toBytes()]
+        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
+        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+        def sendmail_html          = sendmail_template.toString()
+
+        // Send the HTML e-mail
+        Map colors = logColours(params.monochrome_logs)
+        if (email_address) {
+            try {
+                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+                // Try to send HTML e-mail using sendmail
+                [ 'sendmail', '-t' ].execute() << sendmail_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+            } catch (all) {
+                // Catch failures and try with plaintext
+                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                    mail_cmd += [ '-A', mqc_report ]
+                }
+                mail_cmd.execute() << email_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            }
+        }
+
+        // Write summary e-mail HTML to a file
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+        def output_hf = new File(output_d, "pipeline_report.html")
+        output_hf.withWriter { w -> w << email_html }
+        def output_tf = new File(output_d, "pipeline_report.txt")
+        output_tf.withWriter { w -> w << email_txt }
+    }
+
+    //
+    // Print pipeline summary on completion
+    //
+    public static void summary(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+
+        if (workflow.success) {
+            if (workflow.stats.ignoredCount == 0) {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+            } else {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            }
+        } else {
+            hostName(workflow, params, log)
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+        }
+    }
+
+    //
+    // ANSII Colours used for terminal logging
+    //
+    public static Map logColours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+
+        // Reset / Meta
+        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+        // Regular Colors
+        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+        // Bold
+        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+        // Underline
+        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+        // High Intensity
+        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+        // Bold High Intensity
+        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+        return colorcodes
+    }
+
+    //
+    // Does what is says on the tin
+    //
+    public static String dashedLine(monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    //
+    // nf-core logo
+    //
+    public static String logo(workflow, monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        String.format(
+            """\n
+            ${dashedLine(monochrome_logs)}
+                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}
+                  ${colors.white}____${colors.reset}
+                ${colors.white}.´ _  `.${colors.reset}
+               ${colors.white}/  ${colors.green}|\\${colors.reset}`-_ \\${colors.reset}     ${colors.blue} __        __   ___     ${colors.reset}
+              ${colors.white}|   ${colors.green}| \\${colors.reset}  `-|${colors.reset}    ${colors.blue}|__`  /\\  |__) |__  |__/${colors.reset}
+               ${colors.white}\\ ${colors.green}|   \\${colors.reset}  /${colors.reset}     ${colors.blue}.__| /¯¯\\ |  \\ |___ |  \\${colors.reset}
+                ${colors.white}`${colors.green}|${colors.reset}____${colors.green}\\${colors.reset}´${colors.reset}
+
+            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${dashedLine(monochrome_logs)}
+            """.stripIndent()
+        )
+    }
+}
diff --git a/lib/Schema.groovy b/lib/Schema.groovy
deleted file mode 100644
index c2cad355a5..0000000000
--- a/lib/Schema.groovy
+++ /dev/null
@@ -1,228 +0,0 @@
-/*
- * This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
- */
-
-import groovy.json.JsonSlurper
-
-class Schema {
-    /*
-     * This method tries to read a JSON params file
-     */
-    private static LinkedHashMap params_load(String json_schema) {
-        def params_map = new LinkedHashMap()
-        try {
-            params_map = params_read(json_schema)
-        } catch (Exception e) {
-            println "Could not read parameters settings from JSON. $e"
-            params_map = new LinkedHashMap()
-        }
-        return params_map
-    }
-
-    /*
-    Method to actually read in JSON file using Groovy.
-    Group (as Key), values are all parameters
-        - Parameter1 as Key, Description as Value
-        - Parameter2 as Key, Description as Value
-        ....
-    Group
-        -
-    */
-    private static LinkedHashMap params_read(String json_schema) throws Exception {
-        def json = new File(json_schema).text
-        def Map json_params = (Map) new JsonSlurper().parseText(json).get('definitions')
-        /* Tree looks like this in nf-core schema
-         * definitions <- this is what the first get('definitions') gets us
-             group 1
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-                   parameter 2
-                     type
-                     description
-             group 2
-               title
-               description
-                 properties
-                   parameter 1
-                     type
-                     description
-        */
-        def params_map = new LinkedHashMap()
-        json_params.each { key, val ->
-            def Map group = json_params."$key".properties // Gets the property object of the group
-            def title = json_params."$key".title
-            def sub_params = new LinkedHashMap()
-            group.each { innerkey, value ->
-                sub_params.put(innerkey, value)
-            }
-            params_map.put(title, sub_params)
-        }
-        return params_map
-    }
-
-    /*
-     * Get maximum number of characters across all parameter names
-     */
-    private static Integer params_max_chars(params_map) {
-        Integer max_chars = 0
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (param.size() > max_chars) {
-                    max_chars = param.size()
-                }
-            }
-        }
-        return max_chars
-    }
-
-    /*
-     * Beautify parameters for --help
-     */
-    private static String params_help(workflow, params, json_schema, command) {
-        String output  = Headers.nf_core(workflow, params.monochrome_logs) + "\n"
-        output        += "Typical pipeline command:\n\n"
-        output        += "    ${command}\n\n"
-        def params_map = params_load(json_schema)
-        def max_chars  = params_max_chars(params_map) + 1
-        for (group in params_map.keySet()) {
-            output += group + "\n"
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                def type = "[" + group_params.get(param).type + "]"
-                def description = group_params.get(param).description
-                output += "    \u001B[1m--" +  param.padRight(max_chars) + "\u001B[1m" + type.padRight(10) + description + "\n"
-            }
-            output += "\n"
-        }
-        output += Headers.dashed_line(params.monochrome_logs)
-        output += "\n\n" + Checks.citation(workflow)
-        output += "\n\n" + Headers.dashed_line(params.monochrome_logs)
-        return output
-    }
-
-    /*
-     * Groovy Map summarising parameters/workflow options used by the pipeline
-     */
-    private static LinkedHashMap params_summary_map(workflow, params, json_schema) {
-        // Get a selection of core Nextflow workflow options
-        def Map workflow_summary = [:]        
-        if (workflow.revision) {
-            workflow_summary['revision'] = workflow.revision
-        }
-        workflow_summary['runName']      = workflow.runName
-        if (workflow.containerEngine) {
-            workflow_summary['containerEngine'] = "$workflow.containerEngine"
-        }
-        if (workflow.container) {
-            workflow_summary['container']       = "$workflow.container"
-        }
-        workflow_summary['launchDir']    = workflow.launchDir
-        workflow_summary['workDir']      = workflow.workDir
-        workflow_summary['projectDir']   = workflow.projectDir
-        workflow_summary['userName']     = workflow.userName
-        workflow_summary['profile']      = workflow.profile
-        workflow_summary['configFiles']  = workflow.configFiles.join(', ')
-        
-        // Get pipeline parameters defined in JSON Schema
-        def Map params_summary = [:]
-        def blacklist  = ['hostnames']
-        def params_map = params_load(json_schema)
-        for (group in params_map.keySet()) {
-            def sub_params = new LinkedHashMap()
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            for (param in group_params.keySet()) {
-                if (params.containsKey(param) && !blacklist.contains(param)) {
-                    def params_value = params.get(param)
-                    def schema_value = group_params.get(param).default
-                    def param_type   = group_params.get(param).type
-                    if (schema_value == null) {
-                        if (param_type == 'boolean') {
-                            schema_value = false
-                        }
-                        if (param_type == 'string') {
-                            schema_value = ''
-                        }
-                        if (param_type == 'integer') {
-                            schema_value = 0
-                        }
-                    } else {
-                        if (param_type == 'string') {
-                            if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
-                                def sub_string = schema_value.replace('\$projectDir','')
-                                sub_string     = sub_string.replace('\${projectDir}','')
-                                if (params_value.contains(sub_string)) {
-                                    schema_value = params_value
-                                }
-                            }
-                            if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
-                                def sub_string = schema_value.replace('\$params.outdir','')
-                                sub_string     = sub_string.replace('\${params.outdir}','')
-                                if ("${params.outdir}${sub_string}" == params_value) {
-                                    schema_value = params_value
-                                }
-                            }
-                        }
-                    }
-
-                    if (params_value != schema_value) {
-                        sub_params.put("$param", params_value)
-                    }
-                }
-            }
-            params_summary.put(group, sub_params)
-        }
-        return [ 'Core Nextflow options' : workflow_summary ] << params_summary
-    }
-
-    /*
-     * Beautify parameters for summary and return as string
-     */
-    private static String params_summary_log(workflow, params, json_schema) {
-        String output  = Headers.nf_core(workflow, params.monochrome_logs) + "\n"
-        def params_map = params_summary_map(workflow, params, json_schema)
-        def max_chars  = params_max_chars(params_map)
-        for (group in params_map.keySet()) {
-            def group_params = params_map.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                output += group + "\n"
-                for (param in group_params.keySet()) {
-                    output += "    \u001B[1m" +  param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + "\n"
-                }
-                output += "\n"
-            }
-        }
-        output += Headers.dashed_line(params.monochrome_logs)
-        output += "\n\n" + Checks.citation(workflow)
-        output += "\n\n" + Headers.dashed_line(params.monochrome_logs)
-        return output
-    }
-
-    static String params_summary_multiqc(workflow, summary) {
-        String summary_section = ''
-        for (group in summary.keySet()) {
-            def group_params = summary.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                for (param in group_params.keySet()) {
-                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-        yaml_file_text        += "plot_type: 'html'\n"
-        yaml_file_text        += "data: |\n"
-        yaml_file_text        += "${summary_section}"
-        return yaml_file_text
-    }
-}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
new file mode 100644
index 0000000000..18173e9850
--- /dev/null
+++ b/lib/Utils.groovy
@@ -0,0 +1,47 @@
+//
+// This file holds several Groovy functions that could be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class Utils {
+
+    //
+    // When running with -profile conda, warn if channels have not been set-up appropriately
+    //
+    public static void checkCondaChannels(log) {
+        Yaml parser = new Yaml()
+        def channels = []
+        try {
+            def config = parser.load("conda config --show channels".execute().text)
+            channels = config.channels
+        } catch(NullPointerException | IOException e) {
+            log.warn "Could not verify conda channel configuration."
+            return
+        }
+
+        // Check that all channels are present
+        def required_channels = ['conda-forge', 'bioconda', 'defaults']
+        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+
+        // Check that they are in the right order
+        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
+        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+
+        if (conda_check_failed) {
+            log.warn "=============================================================================\n" +
+                "  There is a problem with your Conda configuration!\n\n" +
+                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
+                "  NB: The order of the channels matters!\n" +
+                "==================================================================================="
+        }
+    }
+
+    //
+    // Join module args with appropriate spacing
+    //
+    public static String joinModuleArgs(args_list) {
+        return ' ' + args_list.join(' ')
+    }
+}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
new file mode 100644
index 0000000000..0de4abda18
--- /dev/null
+++ b/lib/WorkflowMain.groovy
@@ -0,0 +1,88 @@
+//
+// This file holds several functions specific to the main.nf workflow in the nf-core/sarek pipeline
+//
+
+class WorkflowMain {
+
+    //
+    // Citation string for pipeline
+    //
+    public static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            "* The pipeline\n" + 
+            "  https://doi.org/10.12688/f1000research.16665.2\n" +
+            "  https://doi.org/10.5281/zenodo.4468605\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
+    //
+    // Print help to screen if required
+    //
+    public static String help(workflow, params, log) {
+        def command = "nextflow run nf-core/sarek --input sample.tsv --genome GRCh38 -profile docker"
+        def help_string = ''
+        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
+        help_string += '\n' + citation(workflow) + '\n'
+        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return help_string
+    }
+
+    //
+    // Print parameter summary log to screen
+    //
+    public static String paramsSummaryLog(workflow, params, log) {
+        def summary_log = ''
+        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
+        summary_log += '\n' + citation(workflow) + '\n'
+        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return summary_log
+    }
+
+    //
+    // Validate parameters and print summary to screen
+    //
+    public static void initialise(workflow, params, log) {
+        // Print help to screen if required
+        if (params.help) {
+            log.info help(workflow, params, log)
+            System.exit(0)
+        }
+
+        // Validate workflow parameters via the JSON schema
+        if (params.validate_params) {
+            NfcoreSchema.validateParameters(workflow, params, log)
+        }
+
+        // Print parameter summary log to screen
+        log.info paramsSummaryLog(workflow, params, log)
+
+        // Check that conda channels are set-up correctly
+        if (params.enable_conda) {
+            Utils.checkCondaChannels(log)
+        }
+
+        // Check AWS batch settings
+        NfcoreTemplate.awsBatch(workflow, params)
+
+        // Check the hostnames against configured profiles
+        NfcoreTemplate.hostName(workflow, params, log)
+    }
+
+    //
+    // Get attribute from genome config file e.g. fasta
+    //
+    public static String getGenomeAttribute(params, attribute) {
+        def val = ''
+        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+            if (params.genomes[ params.genome ].containsKey(attribute)) {
+                val = params.genomes[ params.genome ][ attribute ]
+            }
+        }
+        return val
+    }
+}
diff --git a/lib/WorkflowSarek.groovy b/lib/WorkflowSarek.groovy
new file mode 100644
index 0000000000..37632d5ba8
--- /dev/null
+++ b/lib/WorkflowSarek.groovy
@@ -0,0 +1,25 @@
+//
+// This file holds several functions specific to the main.nf workflow in the nf-core/sarek pipeline
+//
+
+class WorkflowSarek {
+
+    public static void initialise(params, log) {
+        genomeExistsError(params, log)
+
+    }
+
+    //
+    // Exit pipeline if incorrect --genome key provided
+    //
+    private static void genomeExistsError(params, log) {
+        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+            log.error "=============================================================================\n" +
+                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+                "  Currently, the available genome keys are:\n" +
+                "  ${params.genomes.keySet().join(", ")}\n" +
+                "==================================================================================="
+            System.exit(1)
+        }
+    }
+}
\ No newline at end of file
diff --git a/main.nf b/main.nf
index 0c77129ce8..df57dd1b88 100644
--- a/main.nf
+++ b/main.nf
@@ -1,97 +1,87 @@
 #!/usr/bin/env nextflow
 
 /*
---------------------------------------------------------------------------------
-                                  nf-core/sarek
---------------------------------------------------------------------------------
-Started March 2016.
-Ported to nf-core May 2019.
-Ported to DSL 2 July 2020.
---------------------------------------------------------------------------------
-nf-core/sarek:
-  An open-source analysis pipeline to detect germline or somatic variants
-  from whole genome or targeted sequencing
---------------------------------------------------------------------------------
- @Homepage
- https://nf-co.re/sarek
---------------------------------------------------------------------------------
- @Documentation
- https://nf-co.re/sarek/latest/usage
---------------------------------------------------------------------------------
+========================================================================================
+    nf-core/sarek
+========================================================================================
+    Started March 2016.
+    Ported to nf-core May 2019.
+    Ported to DSL 2 July 2020.
+----------------------------------------------------------------------------------------
+    nf-core/sarek:
+        An open-source analysis pipeline to detect germline or somatic variants
+        from whole genome or targeted sequencing
+----------------------------------------------------------------------------------------
+    @Homepage
+    https://nf-co.re/sarek
+----------------------------------------------------------------------------------------
+    @Documentation
+    https://nf-co.re/sarek/usage
+----------------------------------------------------------------------------------------
+    @Github
+    https://github.com/nf-core/sarek
+----------------------------------------------------------------------------------------
+    @Slack
+    https://nfcore.slack.com/channels/sarek
+----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl=2
+nextflow.enable.dsl = 2
 
-////////////////////////////////////////////////////
-/* --               PRINT HELP                 -- */
-////////////////////////////////////////////////////
-
-def json_schema = "$projectDir/nextflow_schema.json"
-if (params.help) {
-    def command = "nextflow run nf-core/sarek -profile docker --input sample.tsv --genome GRCh38"
-    log.info Schema.params_help(workflow, params, json_schema, command)
-    exit 0
-}
-
-////////////////////////////////////////////////////
-/* --          PARAMETER CHECKS                -- */
-////////////////////////////////////////////////////
-
-// Check that conda channels are set-up correctly
-if (params.enable_conda) {
-    Checks.check_conda_channels(log)
-}
+/*
+========================================================================================
+    GENOME PARAMETER VALUES
+========================================================================================
+*/
 
-// Check AWS batch settings
-Checks.aws_batch(workflow, params)
+params.ac_loci                 = WorkflowMain.getGenomeAttribute(params, 'ac_loci')
+params.ac_loci_gc              = WorkflowMain.getGenomeAttribute(params, 'ac_loci_gc')
+params.bwa                     = WorkflowMain.getGenomeAttribute(params, 'bwa')
+params.chr_dir                 = WorkflowMain.getGenomeAttribute(params, 'chr_dir')
+params.chr_length              = WorkflowMain.getGenomeAttribute(params, 'chr_length')
+params.dbsnp                   = WorkflowMain.getGenomeAttribute(params, 'dbsnp')
+params.dbsnp_index             = WorkflowMain.getGenomeAttribute(params, 'dbsnp_index')
+params.dict                    = WorkflowMain.getGenomeAttribute(params, 'dict')
+params.fasta                   = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.fasta_fai               = WorkflowMain.getGenomeAttribute(params, 'fasta_fai')
+params.germline_resource       = WorkflowMain.getGenomeAttribute(params, 'germline_resource')
+params.germline_resource_index = WorkflowMain.getGenomeAttribute(params, 'germline_resource_index')
+params.intervals               = WorkflowMain.getGenomeAttribute(params, 'intervals')
+params.known_indels            = WorkflowMain.getGenomeAttribute(params, 'known_indels')
+params.known_indels_index      = WorkflowMain.getGenomeAttribute(params, 'known_indels_index')
+params.mappability             = WorkflowMain.getGenomeAttribute(params, 'mappability')
+params.snpeff_db               = WorkflowMain.getGenomeAttribute(params, 'snpeff_db')
+params.species                 = WorkflowMain.getGenomeAttribute(params, 'species')
+params.vep_cache_version       = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version')
 
-// Check the hostnames against configured profiles
-Checks.hostname(workflow, params, log)
 
-// Check genome key exists if provided
-Checks.genome_exists(params, log)
+/*
+========================================================================================
+    VALIDATE & PRINT PARAMETER SUMMARY
+========================================================================================
+*/
 
-////////////////////////////////////////////////////
-/* --        REFERENCES PARAMETER VALUES       -- */
-////////////////////////////////////////////////////
-/* -- Initialize each params in params.genomes -- */
-/* --  catch the command line first if defined -- */
-////////////////////////////////////////////////////
+WorkflowMain.initialise(workflow, params, log)
 
-params.ac_loci                 = Checks.get_genome_attribute(params, 'ac_loci')
-params.ac_loci_gc              = Checks.get_genome_attribute(params, 'ac_loci_gc')
-params.bwa                     = Checks.get_genome_attribute(params, 'bwa')
-params.chr_dir                 = Checks.get_genome_attribute(params, 'chr_dir')
-params.chr_length              = Checks.get_genome_attribute(params, 'chr_length')
-params.dbsnp                   = Checks.get_genome_attribute(params, 'dbsnp')
-params.dbsnp_index             = Checks.get_genome_attribute(params, 'dbsnp_index')
-params.dict                    = Checks.get_genome_attribute(params, 'dict')
-params.fasta                   = Checks.get_genome_attribute(params, 'fasta')
-params.fasta_fai               = Checks.get_genome_attribute(params, 'fasta_fai')
-params.germline_resource       = Checks.get_genome_attribute(params, 'germline_resource')
-params.germline_resource_index = Checks.get_genome_attribute(params, 'germline_resource_index')
-params.intervals               = Checks.get_genome_attribute(params, 'intervals')
-params.known_indels            = Checks.get_genome_attribute(params, 'known_indels')
-params.known_indels_index      = Checks.get_genome_attribute(params, 'known_indels_index')
-params.mappability             = Checks.get_genome_attribute(params, 'mappability')
-params.snpeff_db               = Checks.get_genome_attribute(params, 'snpeff_db')
-params.species                 = Checks.get_genome_attribute(params, 'species')
-params.vep_cache_version       = Checks.get_genome_attribute(params, 'vep_cache_version')
 
-////////////////////////////////////////////////////
-/* --         PRINT PARAMETER SUMMARY          -- */
-////////////////////////////////////////////////////
+/*
+========================================================================================
+    NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
 
-def summary_params = Schema.params_summary_map(workflow, params, json_schema)
-log.info Schema.params_summary_log(workflow, params, json_schema)
+workflow NFCORE_SAREK {
+    include { SAREK } from './workflows/sarek'
+    SAREK ()
+}
 
-////////////////////////////////////////////////////
-/* --             RUN THE WORKFLOW             -- */
-////////////////////////////////////////////////////
+/*
+========================================================================================
+    RUN ALL WORKFLOWS
+========================================================================================
+*/
 
+// WORKFLOW: Execute a single named workflow for the pipeline
 workflow {
-
-    include { SAREK } from './workflows/sarek' addParams( summary_params: summary_params )
-    SAREK ()
-
-}
+    NFCORE_SAREK ()
+}
\ No newline at end of file
diff --git a/modules/local/build_intervals/functions.nf b/modules/local/build_intervals/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/local/build_intervals/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/local/build_intervals.nf b/modules/local/build_intervals/main.nf
similarity index 73%
rename from modules/local/build_intervals.nf
rename to modules/local/build_intervals/main.nf
index 10cb148df7..786c04bab4 100644
--- a/modules/local/build_intervals.nf
+++ b/modules/local/build_intervals/main.nf
@@ -2,13 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BUILD_INTERVALS {
     tag "$fai"
     label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:"false") }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -18,10 +19,10 @@ process BUILD_INTERVALS {
     }
 
     input:
-        path fai
+    path fai
 
     output:
-        path "${fai.baseName}.bed"
+    path "${fai.baseName}.bed"
 
     script:
     """
diff --git a/modules/local/concat_vcf.nf b/modules/local/concat_vcf.nf
deleted file mode 100644
index be8f3684ab..0000000000
--- a/modules/local/concat_vcf.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process CONCAT_VCF {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::htslib=1.12" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/htslib:1.12--hd3b49d5_0"
-    } else {
-        container "quay.io/biocontainers/htslib:1.12--hd3b49d5_0"
-    }
-
-    input:
-        tuple val(meta), path(vcf)
-        path fai
-        path bed
-
-    output:
-        tuple val(meta), path("*_*.vcf.gz"), path("*_*.vcf.gz.tbi"), emit: vcf
-
-    script:
-    name = options.suffix ? "${options.suffix}_${meta.id}" : "${meta.id}"
-    target_options = params.target_bed ? "-t ${bed}" : ""
-    interval_options = params.no_intervals ? "-n" : ""
-    """
-    concatenateVCFs.sh -i ${fai} -c ${task.cpus} -o ${name}.vcf ${target_options} ${interval_options}
-    """
-}
\ No newline at end of file
diff --git a/modules/local/concat_vcf/functions.nf b/modules/local/concat_vcf/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/local/concat_vcf/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/local/concat_vcf/main.nf b/modules/local/concat_vcf/main.nf
new file mode 100644
index 0000000000..02a336dda3
--- /dev/null
+++ b/modules/local/concat_vcf/main.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process CONCAT_VCF {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::htslib=1.12" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/htslib:1.12--hd3b49d5_0"
+    } else {
+        container "quay.io/biocontainers/htslib:1.12--hd3b49d5_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+    path fai
+    path bed
+
+    output:
+    tuple val(meta), path("*_*.vcf.gz"), path("*_*.vcf.gz.tbi"), emit: vcf
+
+    script:
+    def prefix           = options.suffix ? "${options.suffix}_${meta.id}" : "${meta.id}"
+    def target_options   = params.target_bed ? "-t ${bed}" : ""
+    def interval_options = params.no_intervals ? "-n" : ""
+    """
+    concatenateVCFs.sh -i ${fai} -c ${task.cpus} -o ${prefix}.vcf ${target_options} ${interval_options}
+    """
+}
\ No newline at end of file
diff --git a/modules/local/create_intervals_bed/functions.nf b/modules/local/create_intervals_bed/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/local/create_intervals_bed/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/local/create_intervals_bed.nf b/modules/local/create_intervals_bed/main.nf
similarity index 79%
rename from modules/local/create_intervals_bed.nf
rename to modules/local/create_intervals_bed/main.nf
index e7554040ff..fb93f04ee4 100644
--- a/modules/local/create_intervals_bed.nf
+++ b/modules/local/create_intervals_bed/main.nf
@@ -1,14 +1,15 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; has_extension } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process CREATE_INTERVALS_BED {
     tag "$intervals"
     label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:"false") }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -18,15 +19,15 @@ process CREATE_INTERVALS_BED {
     }
 
     input:
-        path intervals
+    path intervals
 
     output:
-        path ('*.bed')
+    path ('*.bed')
 
     script:
     // If the interval file is BED format, the fifth column is interpreted to
     // contain runtime estimates, which is then used to combine short-running jobs
-    if (has_extension(intervals, "bed"))
+    if (intervals.toString().toLowerCase().endsWith("bed"))
         """
         awk -vFS="\t" '{
           t = \$5  # runtime estimate
@@ -46,7 +47,7 @@ process CREATE_INTERVALS_BED {
           print \$0 > name
         }' ${intervals}
         """
-    else if (has_extension(intervals, "interval_list"))
+    else if (intervals.toString().toLowerCase().endsWith("interval_list"))
         """
         grep -v '^@' ${intervals} | awk -vFS="\t" '{
           name = sprintf("%s_%d-%d", \$1, \$2, \$3);
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
deleted file mode 100644
index c4a9d6baaa..0000000000
--- a/modules/local/functions.nf
+++ /dev/null
@@ -1,328 +0,0 @@
-/*
- * This file holds several functions used to perform operation in Sarek
- */
- 
-// Check if a row has the expected number of item
-def check_number_of_item(row, number) {
-    if (row.size() != number) exit 1, "Malformed row in TSV file: ${row}, see --help for more information"
-    return true
-}
-
-// Check parameter existence
-def check_parameter_existence(it, list) {
-    if (!list.contains(it)) {
-        log.warn "Unknown parameter: ${it}"
-        return false
-    }
-    return true
-}
-
-// Compare each parameter with a list of parameters
-def check_parameter_list(list, realList) {
-    return list.every{ check_parameter_existence(it, realList) }
-}
-
-// Define list of available tools to annotate
-def define_anno_list() {
-    return [
-        'haplotypecaller',
-        'manta',
-        'mutect2',
-        'strelka',
-        'tiddit'
-    ]
-}
-
-// Define list of skipable QC tools
-def define_skip_qc_list() {
-    return [
-        'bamqc',
-        'baserecalibrator',
-        'bcftools',
-        'documentation',
-        'fastqc',
-        'markduplicates',
-        'multiqc',
-        'samtools',
-        'sentieon',
-        'vcftools',
-        'versions'
-    ]
-}
-
-// Define list of available step
-def define_step_list() {
-    return [
-        'annotate',
-        'controlfreec',
-        'mapping',
-        'preparerecalibration',
-        'recalibrate',
-        'variantcalling'
-    ]
-}
-
-// Define list of available tools
-def define_tool_list() {
-    return [
-        'ascat',
-        'cnvkit',
-        'controlfreec',
-        'dnascope',
-        'dnaseq',
-        'freebayes',
-        'haplotypecaller',
-        'manta',
-        'merge',
-        'mpileup',
-        'mutect2',
-        'snpeff',
-        'strelka',
-        'tiddit',
-        'tnscope',
-        'vep',
-        'msisensor'
-    ]
-}
-
-// Channeling the TSV file containing BAM.
-// Format is: "patient gender status sample bam bai"
-def extract_bam(tsvFile) {
-    Channel.from(tsvFile)
-        .splitCsv(sep: '\t')
-        .map { row ->
-            check_number_of_item(row, 6)
-            def meta = [:]
-
-            meta.patient = row[0]
-            meta.gender  = row[1]
-            meta.status  = return_status(row[2].toInteger())
-            meta.sample  = row[3]
-            meta.id      = meta.sample
-            def bam      = return_file(row[4])
-            def bai      = return_file(row[5])
-
-            if (!has_extension(bam, "bam")) exit 1, "File: ${bam} has the wrong extension. See --help for more information"
-            if (!has_extension(bai, "bai")) exit 1, "File: ${bai} has the wrong extension. See --help for more information"
-
-            return [meta, bam, bai]
-        }
-}
-
-// Create a channel of germline FASTQs from a directory pattern: "my_samples/*/"
-// All FASTQ files in subdirectories are collected and emitted;
-// they must have _R1_ and _R2_ in their names.
-// All FASTQ files are assumed to be from the same sample.
-def extract_fastq_from_dir(folder) {
-    sample = file(folder).getFileName().toString()
-
-    fastq = Channel.fromFilePairs(folder + '/*{_R1_,_R2_}*.fastq.gz')
-        .ifEmpty { error "No directories found matching folder '${folder}'" }
-
-// TODO check if flowcellLane_from_fastq is useful or not
-
-    fastq = fastq.map{ run, pair ->
-        def meta = [:]
-        meta.patient    = sample
-        meta.sample     = meta.patient
-        meta.gender     = 'ZZ' // unused
-        meta.status     = 0    // normal (not tumor)
-        meta.run        = run
-        meta.id         = "${meta.sample}-${meta.run}"
-        def read1       = pair[0]
-        def read2       = pair[1]
-        def CN          = params.sequencing_center ? "CN:${params.sequencing_center}\\t" : ""
-        def read_group  = "\"@RG\\tID:${meta.run}\\t${CN}PU:${meta.run}\\tSM:${meta.sample}\\tLB:${meta.sample}\\tPL:ILLUMINA\""
-        meta.read_group = read_group
-
-        return [meta, [read1, read2]]
-    }
-}
-
-// Channeling the TSV file containing FASTQ or BAM
-// Format is: "patient gender status sample lane fastq1 fastq2"
-// or: "patient gender status sample lane bam"
-def extract_fastq(tsvFile) {
-    Channel.from(tsvFile)
-        .splitCsv(sep: '\t')
-        .map { row ->
-            def meta = [:]
-            meta.patient    = row[0]
-            meta.gender     = row[1]
-            meta.status     = return_status(row[2].toInteger())
-            meta.sample     = row[3]
-            meta.run        = row[4]
-            meta.id         = "${meta.sample}-${meta.run}"
-            def read1       = return_file(row[5])
-            def read2       = "null"
-            def CN          = params.sequencing_center ? "CN:${params.sequencing_center}\\t" : ""
-            def read_group  = "\"@RG\\tID:${meta.run}\\t${CN}PU:${meta.run}\\tSM:${meta.sample}\\tLB:${meta.sample}\\tPL:ILLUMINA\""
-            meta.read_group = read_group
-
-            if (has_extension(read1, "fastq.gz") || has_extension(read1, "fq.gz") || has_extension(read1, "fastq") || has_extension(read1, "fq")) {
-                check_number_of_item(row, 7)
-                read2 = return_file(row[6])
-            if (!has_extension(read2, "fastq.gz") && !has_extension(read2, "fq.gz")  && !has_extension(read2, "fastq") && !has_extension(read2, "fq")) exit 1, "File: ${file2} has the wrong extension. See --help for more information"
-            if (has_extension(read1, "fastq") || has_extension(read1, "fq") || has_extension(read2, "fastq") || has_extension(read2, "fq")) {
-                exit 1, "We do recommend to use gziped fastq file to help you reduce your data footprint."
-            }
-        }
-        else if (has_extension(read1, "bam")) check_number_of_item(row, 6)
-        else exit 1, "No recognisable extention for input file: ${read1}"
-
-        return [meta, [read1, read2]]
-    }
-}
-
-// // Channeling the TSV file containing mpileup
-// // Format is: "patient gender status sample pileup"
-// def extract_pileup(tsvFile) {
-//     Channel.from(tsvFile)
-//         .splitCsv(sep: '\t')
-//         .map { row ->
-//             check_number_of_item(row, 5)
-//             def idPatient = row[0]
-//             def gender    = row[1]
-//             def status    = return_status(row[2].toInteger())
-//             def idSample  = row[3]
-//             def mpileup   = return_file(row[4])
-
-//             if (!has_extension(mpileup, "pileup")) exit 1, "File: ${mpileup} has the wrong extension. See --help for more information"
-
-//             return [idPatient, gender, status, idSample, mpileup]
-//         }
-// }
-
-// Channeling the TSV file containing Recalibration Tables.
-// Format is: "patient gender status sample bam bai recalTable"
-def extract_recal(tsvFile) {
-    Channel.from(tsvFile)
-        .splitCsv(sep: '\t')
-        .map { row ->
-            check_number_of_item(row, 7)
-            def meta = [:]
-
-            meta.patient = row[0]
-            meta.gender  = row[1]
-            meta.status  = return_status(row[2].toInteger())
-            meta.sample  = row[3]
-            meta.id      = meta.sample
-            def bam      = return_file(row[4])
-            def bai      = return_file(row[5])
-            def table    = return_file(row[6])
-
-            if (!has_extension(bam, "bam")) exit 1, "File: ${bam} has the wrong extension. See --help for more information"
-            if (!has_extension(bai, "bai")) exit 1, "File: ${bai} has the wrong extension. See --help for more information"
-            if (!has_extension(table, "recal.table")) exit 1, "File: ${table} has the wrong extension. See --help for more information"
-
-            return [meta, bam, bai, table]
-        }
-}
-
-// // Parse first line of a FASTQ file, return the flowcell id and lane number.
-// def flowcellLane_from_fastq(path) {
-//     // expected format:
-//     // xx:yy:FLOWCELLID:LANE:... (seven fields)
-//     // or
-//     // FLOWCELLID:LANE:xx:... (five fields)
-//     InputStream fileStream = new FileInputStream(path.toFile())
-//     InputStream gzipStream = new java.util.zip.GZIPInputStream(fileStream)
-//     Reader decoder = new InputStreamReader(gzipStream, 'ASCII')
-//     BufferedReader buffered = new BufferedReader(decoder)
-//     def line = buffered.readLine()
-//     assert line.startsWith('@')
-//     line = line.substring(1)
-//     def fields = line.split(' ')[0].split(':')
-//     String fcid
-//     int lane
-//     if (fields.size() == 7) {
-//         // CASAVA 1.8+ format
-//         fcid = fields[2]
-//         lane = fields[3].toInteger()
-//     } else if (fields.size() == 5) {
-//         fcid = fields[0]
-//         lane = fields[1].toInteger()
-//     }
-//     [fcid, lane]
-// }
-
-// Check file extension
-def has_extension(it, extension) {
-    it.toString().toLowerCase().endsWith(extension.toLowerCase())
-}
-
-// Return file if it exists
-def return_file(it) {
-    if (!file(it).exists()) exit 1, "Missing file in TSV file: ${it}, see --help for more information"
-    return file(it)
-}
-
-// Remove .ann .gz and .vcf extension from a VCF file
-def reduce_vcf(file) {
-    return file.fileName.toString().minus(".ann").minus(".vcf").minus(".gz")
-}
-
-// Return status [0,1]
-// 0 == Normal, 1 == Tumor
-def return_status(it) {
-    if (!(it in [0, 1])) exit 1, "Status is not recognized in TSV file: ${it}, see --help for more information"
-    return it
-}
-
-/*
- * nf-core core functions
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/index_target_bed/functions.nf b/modules/local/index_target_bed/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/local/index_target_bed/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/local/index_target_bed.nf b/modules/local/index_target_bed/main.nf
similarity index 71%
rename from modules/local/index_target_bed.nf
rename to modules/local/index_target_bed/main.nf
index 7411c09398..412f47298c 100644
--- a/modules/local/index_target_bed.nf
+++ b/modules/local/index_target_bed/main.nf
@@ -2,13 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process INDEX_TARGET_BED {
     tag "$target_bed"
     label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:"false") }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::htslib=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -18,10 +19,10 @@ process INDEX_TARGET_BED {
     }
 
     input:
-        path target_bed
+    path target_bed
 
     output:
-        tuple path("${target_bed}.gz"), path("${target_bed}.gz.tbi")
+    tuple path("${target_bed}.gz"), path("${target_bed}.gz.tbi")
 
     script:
     """
diff --git a/modules/nf-core/software/bwa/index/functions.nf b/modules/nf-core/software/bwa/index/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/bwa/index/functions.nf
+++ b/modules/nf-core/software/bwa/index/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/bwa/index/main.nf b/modules/nf-core/software/bwa/index/main.nf
index 915c6623b4..aabd187c91 100644
--- a/modules/nf-core/software/bwa/index/main.nf
+++ b/modules/nf-core/software/bwa/index/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWA_INDEX {
     tag "$fasta"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/bwa/index/meta.yml b/modules/nf-core/software/bwa/index/meta.yml
index 0c3b8f5ff4..181204c3da 100644
--- a/modules/nf-core/software/bwa/index/meta.yml
+++ b/modules/nf-core/software/bwa/index/meta.yml
@@ -13,27 +13,6 @@ tools:
         homepage: http://bio-bwa.sourceforge.net/
         documentation: http://www.htslib.org/doc/samtools.html
         arxiv: arXiv:1303.3997
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - fasta:
         type: file
diff --git a/modules/nf-core/software/bwa/mem/functions.nf b/modules/nf-core/software/bwa/mem/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/bwa/mem/functions.nf
+++ b/modules/nf-core/software/bwa/mem/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/bwa/mem/main.nf b/modules/nf-core/software/bwa/mem/main.nf
index 5d39412d86..8fac539fdb 100644
--- a/modules/nf-core/software/bwa/mem/main.nf
+++ b/modules/nf-core/software/bwa/mem/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWA_MEM {
     tag "$meta.id"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -27,6 +27,7 @@ process BWA_MEM {
     path  "*.version.txt"         , emit: version
 
     script:
+    def split_cpus = Math.floor(task.cpus/2)
     def software   = getSoftwareName(task.process)
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
@@ -36,10 +37,10 @@ process BWA_MEM {
     bwa mem \\
         $options.args \\
         $read_group \\
-        -t $task.cpus \\
+        -t ${split_cpus} \\
         \$INDEX \\
         $reads \\
-        | samtools $options.args2 --threads $task.cpus -o ${prefix}.bam -
+        | samtools $options.args2 --threads ${split_cpus} -o ${prefix}.bam -
 
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
diff --git a/modules/nf-core/software/bwa/mem/meta.yml b/modules/nf-core/software/bwa/mem/meta.yml
index 2e44951c17..693c5450f2 100644
--- a/modules/nf-core/software/bwa/mem/meta.yml
+++ b/modules/nf-core/software/bwa/mem/meta.yml
@@ -16,27 +16,6 @@ tools:
         homepage: http://bio-bwa.sourceforge.net/
         documentation: http://www.htslib.org/doc/samtools.html
         arxiv: arXiv:1303.3997
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
diff --git a/modules/nf-core/software/bwamem2/index/functions.nf b/modules/nf-core/software/bwamem2/index/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/bwamem2/index/functions.nf
+++ b/modules/nf-core/software/bwamem2/index/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/bwamem2/index/main.nf b/modules/nf-core/software/bwamem2/index/main.nf
index 34e8ba469f..b667f266cf 100644
--- a/modules/nf-core/software/bwamem2/index/main.nf
+++ b/modules/nf-core/software/bwamem2/index/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMEM2_INDEX {
     tag "$fasta"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/bwamem2/index/meta.yml b/modules/nf-core/software/bwamem2/index/meta.yml
index 707809028d..9d717f739e 100644
--- a/modules/nf-core/software/bwamem2/index/meta.yml
+++ b/modules/nf-core/software/bwamem2/index/meta.yml
@@ -12,27 +12,6 @@ tools:
             a large reference genome, such as the human genome.
         homepage: https://github.com/bwa-mem2/bwa-mem2
         documentation: https://github.com/bwa-mem2/bwa-mem2#usage
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - fasta:
         type: file
diff --git a/modules/nf-core/software/bwamem2/mem/functions.nf b/modules/nf-core/software/bwamem2/mem/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/bwamem2/mem/functions.nf
+++ b/modules/nf-core/software/bwamem2/mem/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/bwamem2/mem/main.nf b/modules/nf-core/software/bwamem2/mem/main.nf
index 4f2195ac5b..633e62d072 100644
--- a/modules/nf-core/software/bwamem2/mem/main.nf
+++ b/modules/nf-core/software/bwamem2/mem/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMEM2_MEM {
     tag "$meta.id"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -27,6 +27,7 @@ process BWAMEM2_MEM {
     path  "*.version.txt"         , emit: version
 
     script:
+    def split_cpus = Math.floor(task.cpus/2)
     def software   = getSoftwareName(task.process)
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
@@ -36,10 +37,10 @@ process BWAMEM2_MEM {
     bwa-mem2 mem \\
         $options.args \\
         $read_group \\
-        -t $task.cpus \\
+        -t ${split_cpus} \\
         \$INDEX \\
         $reads \\
-        | samtools $options.args2 -@ $task.cpus -o ${prefix}.bam -
+        | samtools $options.args2 -@ ${split_cpus} -o ${prefix}.bam -
 
     echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
     """
diff --git a/modules/nf-core/software/bwamem2/mem/meta.yml b/modules/nf-core/software/bwamem2/mem/meta.yml
index 7d59b9b404..2fc7713d0f 100644
--- a/modules/nf-core/software/bwamem2/mem/meta.yml
+++ b/modules/nf-core/software/bwamem2/mem/meta.yml
@@ -16,27 +16,6 @@ tools:
         homepage: http://bio-bwa.sourceforge.net/
         documentation: http://www.htslib.org/doc/samtools.html
         arxiv: arXiv:1303.3997
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
diff --git a/modules/nf-core/software/fastqc/functions.nf b/modules/nf-core/software/fastqc/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/fastqc/functions.nf
+++ b/modules/nf-core/software/fastqc/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/fastqc/main.nf b/modules/nf-core/software/fastqc/main.nf
index cce410a080..7ce76adffb 100644
--- a/modules/nf-core/software/fastqc/main.nf
+++ b/modules/nf-core/software/fastqc/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process FASTQC {
     tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/fastqc/meta.yml b/modules/nf-core/software/fastqc/meta.yml
index 413aad8db6..8eb9953dce 100644
--- a/modules/nf-core/software/fastqc/meta.yml
+++ b/modules/nf-core/software/fastqc/meta.yml
@@ -15,27 +15,6 @@ tools:
             overrepresented sequences.
         homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
         documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
diff --git a/modules/nf-core/software/functions.nf b/modules/nf-core/software/functions.nf
deleted file mode 100644
index d25eea86b3..0000000000
--- a/modules/nf-core/software/functions.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/nf-core/software/gatk4/applybqsr.nf b/modules/nf-core/software/gatk4/applybqsr.nf
deleted file mode 100644
index cbe83e2f68..0000000000
--- a/modules/nf-core/software/gatk4/applybqsr.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process GATK4_APPLYBQSR {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path(bam), path(bai), path(recalibrationReport), path(interval)
-    path dict
-    path fasta
-    path fai
-
-    output:
-    tuple val(meta), path("${prefix}${meta.sample}.recal.bam") , emit: bam
-    path "*.version.txt" , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    prefix = params.no_intervals ? "" : "${interval.baseName}_"
-    options_intervals = params.no_intervals ? "" : "-L ${interval}"
-    """
-    gatk --java-options -Xmx${task.memory.toGiga()}g \
-        ApplyBQSR \
-        -R ${fasta} \
-        --input ${bam} \
-        --output ${prefix}${meta.sample}.recal.bam \
-        ${options_intervals} \
-        --bqsr-recal-file ${recalibrationReport}
-
-    echo \$(gatk ApplyBQSR --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/applybqsr/functions.nf b/modules/nf-core/software/gatk4/applybqsr/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/applybqsr/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/applybqsr/main.nf b/modules/nf-core/software/gatk4/applybqsr/main.nf
new file mode 100644
index 0000000000..ba0c629869
--- /dev/null
+++ b/modules/nf-core/software/gatk4/applybqsr/main.nf
@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_APPLYBQSR {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(bqsr_table), path(intervalsBed)
+    path fasta
+    path fastaidx
+    path dict
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt",           emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
+    """
+    gatk ApplyBQSR \\
+        -R $fasta \\
+        -I $bam \\
+        --bqsr-recal-file $bqsr_table \\
+        $intervalsCommand \\
+        -O ${prefix}.bam \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}
diff --git a/modules/nf-core/software/gatk4/applybqsr/meta.yml b/modules/nf-core/software/gatk4/applybqsr/meta.yml
new file mode 100644
index 0000000000..9bf12f09bb
--- /dev/null
+++ b/modules/nf-core/software/gatk4/applybqsr/meta.yml
@@ -0,0 +1,58 @@
+name: gatk4_applybqsr
+description: Apply base quality score recalibration (BQSR) to a bam file
+keywords:
+  - bqsr
+  - bam
+tools:
+  - gatk4:
+    description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file from alignment
+      pattern: "*.{bam}"
+  - bqsr_table:
+      type: file
+      description: Recalibration table from gatk4_baserecalibrator
+  - fasta:
+      type: file
+      description: The reference fasta file
+  - fastaidx:
+      type: file
+      description: Index of reference fasta file
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+  - intervalsBed:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: Recalibrated BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@yocra3"
diff --git a/modules/nf-core/software/gatk4/baserecalibrator.nf b/modules/nf-core/software/gatk4/baserecalibrator.nf
deleted file mode 100644
index b6ba407592..0000000000
--- a/modules/nf-core/software/gatk4/baserecalibrator.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process GATK4_BASERECALIBRATOR {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path(bam), path(bai), path(interval)
-    path dbsnp
-    tuple val(meta_dbsnp), path(dbsnp_tbi)
-    path dict
-    path fai
-    path fasta
-    path known_indels
-    tuple val(meta_known_indels), path(known_indels_tbi)
-        
-    output:
-    tuple val(meta), path("${prefix}${meta.sample}.recal.table"), emit: report
-    path "*.version.txt" , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    options_dbsnp = params.dbsnp ? "--known-sites ${dbsnp}" : ""
-    options_intervals = params.no_intervals ? "" : "-L ${interval}"
-    options_known_indels = params.known_indels ? known_indels.collect{"--known-sites ${it}"}.join(' ') : ""
-    prefix = params.no_intervals ? "" : "${interval.baseName}_"
-    // TODO: --use-original-qualities ???
-    """
-    gatk --java-options -Xmx${task.memory.toGiga()}g \
-        BaseRecalibrator \
-        -I ${bam} \
-        -O ${prefix}${meta.sample}.recal.table \
-        --tmp-dir . \
-        -R ${fasta} \
-        ${options_dbsnp} \
-        ${options_known_indels} \
-        ${options_intervals} \
-        --verbosity INFO
-
-    echo \$(gatk ApplyBQSR --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/baserecalibrator/functions.nf b/modules/nf-core/software/gatk4/baserecalibrator/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/baserecalibrator/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/baserecalibrator/main.nf b/modules/nf-core/software/gatk4/baserecalibrator/main.nf
new file mode 100644
index 0000000000..48f05fa21a
--- /dev/null
+++ b/modules/nf-core/software/gatk4/baserecalibrator/main.nf
@@ -0,0 +1,49 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_BASERECALIBRATOR {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(intervalsBed)
+    path fasta
+    path fai
+    path dict
+    path knownSites
+    path knownSites_tbi
+
+    output:
+    tuple val(meta), path("*.table"), emit: table
+    path "*.version.txt" ,            emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
+    def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
+    """
+    gatk BaseRecalibrator  \
+        -R $fasta \
+        -I $bam \
+        $sitesCommand \
+        $intervalsCommand \
+        $options.args \
+        -O ${prefix}.table
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}
diff --git a/modules/nf-core/software/gatk4/baserecalibrator/meta.yml b/modules/nf-core/software/gatk4/baserecalibrator/meta.yml
new file mode 100644
index 0000000000..0996dcbe51
--- /dev/null
+++ b/modules/nf-core/software/gatk4/baserecalibrator/meta.yml
@@ -0,0 +1,58 @@
+name: gatk4_baserecalibrator
+description: Generate recalibration table for Base Quality Score Recalibration (BQSR)
+keywords:
+  - sort
+tools:
+  - gatk4:
+    description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file from alignment
+      pattern: "*.{bam}"
+  - fasta:
+      type: file
+      description: The reference fasta file
+  - fastaidx:
+      type: file
+      description: Index of reference fasta file
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+  - intervalsBed:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+  - knownSites:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - table:
+      type: file
+      description: Recalibration table from BaseRecalibrator
+      pattern: "*.{table}"
+
+authors:
+  - "@yocra3"
diff --git a/modules/nf-core/software/gatk4/createsequencedictionary/functions.nf b/modules/nf-core/software/gatk4/createsequencedictionary/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/gatk4/createsequencedictionary/functions.nf
+++ b/modules/nf-core/software/gatk4/createsequencedictionary/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/gatk4/createsequencedictionary/main.nf b/modules/nf-core/software/gatk4/createsequencedictionary/main.nf
index 5f9a7ce25f..8bc71a8073 100644
--- a/modules/nf-core/software/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/software/gatk4/createsequencedictionary/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/software/gatk4/createsequencedictionary/meta.yml
index b33af6ad26..d0cc59801f 100644
--- a/modules/nf-core/software/gatk4/createsequencedictionary/meta.yml
+++ b/modules/nf-core/software/gatk4/createsequencedictionary/meta.yml
@@ -12,27 +12,6 @@ tools:
         homepage: https://gatk.broadinstitute.org/hc/en-us
         documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
         doi: 10.1158/1538-7445.AM2017-3590
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - fasta:
         type: file
diff --git a/modules/nf-core/software/gatk4/gatherbqsrreports/functions.nf b/modules/nf-core/software/gatk4/gatherbqsrreports/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/gatherbqsrreports/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/gatherbqsrreports.nf b/modules/nf-core/software/gatk4/gatherbqsrreports/main.nf
similarity index 78%
rename from modules/nf-core/software/gatk4/gatherbqsrreports.nf
rename to modules/nf-core/software/gatk4/gatherbqsrreports/main.nf
index bfda3d217b..5f71884bda 100644
--- a/modules/nf-core/software/gatk4/gatherbqsrreports.nf
+++ b/modules/nf-core/software/gatk4/gatherbqsrreports/main.nf
@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
 def options    = initOptions(params.options)
@@ -6,8 +6,9 @@ def options    = initOptions(params.options)
 process GATK4_GATHERBQSRREPORTS {
     tag "$meta.id"
     label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
  
     conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -22,7 +23,7 @@ process GATK4_GATHERBQSRREPORTS {
     output:
     tuple val(meta), path("${meta.sample}.recal.table"), emit: table
     path "${meta.sample}.recal.table",                   emit: report
-    path "*.version.txt" , emit: version
+    path "*.version.txt",                                emit: version
         
     script:
     def software = getSoftwareName(task.process)
diff --git a/modules/nf-core/software/gatk4/genotypegvcf/functions.nf b/modules/nf-core/software/gatk4/genotypegvcf/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/genotypegvcf/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/genotypegvcf.nf b/modules/nf-core/software/gatk4/genotypegvcf/main.nf
similarity index 93%
rename from modules/nf-core/software/gatk4/genotypegvcf.nf
rename to modules/nf-core/software/gatk4/genotypegvcf/main.nf
index 19337680b2..270454b465 100644
--- a/modules/nf-core/software/gatk4/genotypegvcf.nf
+++ b/modules/nf-core/software/gatk4/genotypegvcf/main.nf
@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
 def options    = initOptions(params.options)
@@ -19,7 +19,7 @@ process GATK4_GENOTYPEGVCF {
     input:
     tuple val(meta), path(interval), path(gvcf)
     path dbsnp
-    tuple val(meta_dbsnp), path(dbsnp_tbi)
+    path dbsnp_tbi
     path dict
     path fasta
     path fai
diff --git a/modules/nf-core/software/gatk4/haplotypecaller.nf b/modules/nf-core/software/gatk4/haplotypecaller.nf
deleted file mode 100644
index 818ed0c878..0000000000
--- a/modules/nf-core/software/gatk4/haplotypecaller.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process GATK4_HAPLOTYPECALLER {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path(bam), path(bai), file(interval)
-    path dbsnp
-    tuple val(meta_dbsnp), path(dbsnp_tbi)
-    path dict
-    path fasta
-    path fai
-    val no_intervals
-
-    output:
-    tuple val(meta), path("${interval.baseName}_${meta.id}.g.vcf"),                 emit: gvcf
-    tuple val(meta), path(interval), path("${interval.baseName}_${meta.id}.g.vcf"), emit: interval_gvcf
-    path "*.version.txt" , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    intervalsOptions = no_intervals ? "" : "-L ${interval}"
-    dbsnpOptions = params.dbsnp ? "--D ${dbsnp}" : ""
-    """
-    gatk --java-options "-Xmx${task.memory.toGiga()}g -Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
-        HaplotypeCaller \
-        -R ${fasta} \
-        -I ${bam} \
-        ${intervalsOptions} \
-        ${dbsnpOptions} \
-        -O ${interval.baseName}_${meta.id}.g.vcf \
-        -ERC GVCF
-
-    echo \$(gatk HaplotypeCaller --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
-    """
-}
diff --git a/modules/nf-core/software/gatk4/haplotypecaller/functions.nf b/modules/nf-core/software/gatk4/haplotypecaller/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/haplotypecaller/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/haplotypecaller/main.nf b/modules/nf-core/software/gatk4/haplotypecaller/main.nf
new file mode 100644
index 0000000000..48f73b9340
--- /dev/null
+++ b/modules/nf-core/software/gatk4/haplotypecaller/main.nf
@@ -0,0 +1,58 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_HAPLOTYPECALLER {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir params.outdir, mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(interval)
+    path dbsnp
+    path dbsnp_tbi
+    path dict
+    path fasta
+    path fai
+    val no_intervals
+
+    output:
+    tuple val(meta), path("*.vcf"),                 emit: vcf
+    tuple val(meta), path(interval), path("*.vcf"), emit: interval_vcf
+    path "*.version.txt",                           emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def prefix    = options.suffix ? "${interval.baseName}_${meta.id}${options.suffix}" : "${interval.baseName}_${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    def intervalsOptions = no_intervals ? "" : "-L ${interval}"
+    def dbsnpOptions = params.dbsnp ? "--D ${dbsnp}" : ""
+    """
+    gatk \\
+        --java-options "-Xmx${avail_mem}g" \\
+        HaplotypeCaller \\
+        -R $fasta \\
+        -I $bam \\
+        ${intervalsOptions} \\
+        ${dbsnpOptions} \\
+        -O ${prefix}.vcf \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/haplotypecaller/meta.yml b/modules/nf-core/software/gatk4/haplotypecaller/meta.yml
new file mode 100644
index 0000000000..f0fc3910e3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/haplotypecaller/meta.yml
@@ -0,0 +1,63 @@
+name: gatk4_haplotypecaller
+description: Call germline SNPs and indels via local re-assembly of haplotypes
+keywords:
+  - gatk4
+  - haplotypecaller
+  - haplotype
+tools:
+  - gatk4:
+    description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: Index of BAM file
+      pattern: "*.bam.bai"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: Index of VCF file
+      pattern: "*.vcf.gz.tbi"
+
+authors:
+  - "@suzannejin"
diff --git a/modules/nf-core/software/gatk4/markduplicates.nf b/modules/nf-core/software/gatk4/markduplicates.nf
deleted file mode 100644
index ad976d628a..0000000000
--- a/modules/nf-core/software/gatk4/markduplicates.nf
+++ /dev/null
@@ -1,83 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process GATK4_MARKDUPLICATES {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path("${meta.sample}.bam"), path("${meta.sample}.bam.bai")
-
-    output:
-    tuple val(meta), path("${meta.sample}.md.bam"), path("${meta.sample}.md.bam.bai"), emit: bam
-    path "${meta.sample}.bam.metrics", optional : true,                                emit: report
-    path "*.version.txt" , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    markdup_java_options = task.memory.toGiga() > 8 ? params.markdup_java_options : "\"-Xms" +  (task.memory.toGiga() / 2).trunc() + "g -Xmx" + (task.memory.toGiga() - 1) + "g\""
-    metrics = 'markduplicates' in params.skip_qc ? '' : "-M ${meta.sample}.bam.metrics"
-    """
-    gatk --java-options ${markdup_java_options} \
-        MarkDuplicates \
-        --INPUT ${meta.sample}.bam \
-        --METRICS_FILE ${meta.sample}.bam.metrics \
-        --TMP_DIR . \
-        --ASSUME_SORT_ORDER coordinate \
-        --CREATE_INDEX true \
-        --OUTPUT ${meta.sample}.md.bam
-    mv ${meta.sample}.md.bai ${meta.sample}.md.bam.bai
-
-    echo \$(gatk MarkDuplicates --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
-    """
-}
-
-process GATK4_MARKDUPLICATES_SPARK {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::gatk4-spark=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4-spark:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4-spark:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path("${meta.sample}.bam"), path("${meta.sample}.bam.bai")
-
-    output:
-    tuple val(meta), path("${meta.sample}.md.bam"), path("${meta.sample}.md.bam.bai"), emit: bam
-    path "${meta.sample}.bam.metrics", optional : true,                                emit: report
-    path "*.version.txt" , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    markdup_java_options = task.memory.toGiga() > 8 ? params.markdup_java_options : "\"-Xms" +  (task.memory.toGiga() / 2).trunc() + "g -Xmx" + (task.memory.toGiga() - 1) + "g\""
-    metrics = 'markduplicates' in params.skip_qc ? '' : "-M ${meta.sample}.bam.metrics"
-    """
-    gatk --java-options ${markdup_java_options} \
-        MarkDuplicatesSpark \
-        -I ${meta.sample}.bam \
-        -O ${meta.sample}.md.bam \
-        ${metrics} \
-        --tmp-dir . \
-        --create-output-bam-index true \
-        --spark-master local[${task.cpus}]
-
-    echo \$(gatk MarkDuplicatesSpark --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/markduplicates/functions.nf b/modules/nf-core/software/gatk4/markduplicates/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicates/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/markduplicates/main.nf b/modules/nf-core/software/gatk4/markduplicates/main.nf
new file mode 100644
index 0000000000..751ff82337
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicates/main.nf
@@ -0,0 +1,48 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_MARKDUPLICATES {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val use_metrics
+
+    output:
+    tuple val(meta), path("*.bam"), path("*.bai"),       emit: bam
+    tuple val(meta), path("*.metrics"), optional : true, emit: metrics
+    path "*.version.txt",                                emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def metrics  = use_metrics ? "M=${prefix}.metrics" :''
+    """
+    gatk MarkDuplicates \\
+        I=$bam \\
+        $metrics \
+        TMP_DIR=. \\
+        ASSUME_SORT_ORDER=coordinate \\
+        CREATE_INDEX=true \\
+        O=${prefix}.bam \\
+        $options.args
+
+    mv ${prefix}.bai ${prefix}.bam.bai
+
+    echo \$(gatk MarkDuplicates --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/markduplicates/meta.yml b/modules/nf-core/software/gatk4/markduplicates/meta.yml
new file mode 100644
index 0000000000..abe61e023f
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicates/meta.yml
@@ -0,0 +1,49 @@
+name: gatk4_markduplicates
+description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
+keywords:
+  - markduplicates
+  - bam
+  - sort
+tools:
+  - gatk4:
+      description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Sorted BAM file
+      pattern: "*.{bam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: Marked duplicates BAM file
+      pattern: "*.{bam}"
+  - metrics:
+      type: file
+      description: Duplicate metrics file generated by GATK
+      pattern: "*.{metrics.txt}"
+
+authors:
+  - "@ajodeh-juma"
diff --git a/modules/nf-core/software/gatk4/markduplicatesspark/functions.nf b/modules/nf-core/software/gatk4/markduplicatesspark/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicatesspark/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/gatk4/markduplicatesspark/main.nf b/modules/nf-core/software/gatk4/markduplicatesspark/main.nf
new file mode 100644
index 0000000000..dd8b71f90a
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicatesspark/main.nf
@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_MARKDUPLICATES_SPARK {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4-spark=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4-spark:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4-spark:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val use_metrics
+
+    output:
+    tuple val(meta), path("*.bam"), path("*.bai"),       emit: bam
+    tuple val(meta), path("*.metrics"), optional : true, emit: metrics
+    path "*.version.txt",                                emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def metrics  = use_metrics ? "-M ${prefix}.bam.metrics" :''
+    """
+    gatk MarkDuplicatesSpark \\
+        -I $bam \\
+        $metrics \
+        --tmp-dir . \\
+        --create-output-bam-index true \\
+        --spark-master local[${task.cpus}] \\
+        -O ${prefix}.bam \\
+        $options.args
+
+    echo \$(gatk MarkDuplicatesSpark --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/gatk4/markduplicatesspark/meta.yml b/modules/nf-core/software/gatk4/markduplicatesspark/meta.yml
new file mode 100644
index 0000000000..abe61e023f
--- /dev/null
+++ b/modules/nf-core/software/gatk4/markduplicatesspark/meta.yml
@@ -0,0 +1,49 @@
+name: gatk4_markduplicates
+description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
+keywords:
+  - markduplicates
+  - bam
+  - sort
+tools:
+  - gatk4:
+      description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Sorted BAM file
+      pattern: "*.{bam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: Marked duplicates BAM file
+      pattern: "*.{bam}"
+  - metrics:
+      type: file
+      description: Duplicate metrics file generated by GATK
+      pattern: "*.{metrics.txt}"
+
+authors:
+  - "@ajodeh-juma"
diff --git a/modules/nf-core/software/manta/somatic/functions.nf b/modules/nf-core/software/manta/somatic/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/manta/somatic/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/manta/somatic.nf b/modules/nf-core/software/manta/somatic/main.nf
similarity index 85%
rename from modules/nf-core/software/manta/somatic.nf
rename to modules/nf-core/software/manta/somatic/main.nf
index 8976d423bd..a27d43b2f6 100644
--- a/modules/nf-core/software/manta/somatic.nf
+++ b/modules/nf-core/software/manta/somatic/main.nf
@@ -1,13 +1,15 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MANTA_SOMATIC {
     tag "$meta.id"
     label 'process_high'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -37,16 +39,16 @@ process MANTA_SOMATIC {
     // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
     // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
     //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    options_manta = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    options_manta = params.target_bed ? "--exome --callRegions $target_bed" : ""
     """
     configManta.py \
-        --tumorBam ${bam_tumor} \
-        --normalBam ${bam_normal} \
-        --reference ${fasta} \
-        ${options_manta} \
+        --tumorBam $bam_tumor \
+        --normalBam $bam_normal \
+        --reference $fasta \
+        $options_manta \
         --runDir manta
 
-    python manta/runWorkflow.py -m local -j ${task.cpus}
+    python manta/runWorkflow.py -m local -j $task.cpus
 
     mv manta/results/variants/candidateSmallIndels.vcf.gz     ${prefix}.candidateSmallIndels.vcf.gz
     mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidateSmallIndels.vcf.gz.tbi
diff --git a/modules/nf-core/software/msisensor/msi.nf b/modules/nf-core/software/msisensor/msi.nf
deleted file mode 100644
index 59fa69e4a4..0000000000
--- a/modules/nf-core/software/msisensor/msi.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process MSISENSOR_MSI {
-    tag "$meta.id"
-    label 'process_high'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
-    } else {
-        container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
-    }
-
-    input:
-        tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor)
-        path msisensor_scan
-
-    output:
-        tuple val(meta), path("*.list")
-
-    script:
-    def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
-    def prefix   = ioptions.suffix ? "msisensor_${meta.id}${ioptions.suffix}" : "msisensor_${meta.id}"
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    """
-    msisensor msi -d ${msisensor_scan} \
-                  -b 4 \
-                  -t ${bam_tumor} \
-                  -n ${bam_normal} \
-                  -o ${prefix}
-
-    mv ${prefix}          ${prefix}.list
-    mv ${prefix}_dis      ${prefix}_dis.list
-    mv ${prefix}_germline ${prefix}_germline.list
-    mv ${prefix}_somatic  ${prefix}_somatic.list
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/msisensor/scan.nf b/modules/nf-core/software/msisensor/scan.nf
deleted file mode 100644
index fa71e5b723..0000000000
--- a/modules/nf-core/software/msisensor/scan.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process MSISENSOR_SCAN {
-    tag "$fasta"
-    label 'process_high'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:"false") }
-
-    conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
-    } else {
-        container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
-    }
-
-    input:
-        path fasta
-        path fai
-
-    output:
-        path "microsatellites.list"
-
-    script:
-    def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
-    def prefix   = ioptions.suffix ? "msisensor_${ioptions.suffix}" : "msisensor_"
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    """
-    msisensor scan -d ${fasta} -o microsatellites.list
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/msisensorpro/msi/functions.nf b/modules/nf-core/software/msisensorpro/msi/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/msi/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/msisensorpro/msi/main.nf b/modules/nf-core/software/msisensorpro/msi/main.nf
new file mode 100644
index 0000000000..01c9553a62
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/msi/main.nf
@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MSISENSORPRO_MSI {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::msisensor-pro=1.1.a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/msisensor-pro:1.1.a--hb3646a4_0"
+    } else {
+        container "quay.io/biocontainers/msisensor-pro:1.1.a--hb3646a4_0"
+    }
+
+    input:
+        tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor)
+        path msisensorpro_scan
+
+    output:
+        tuple val(meta), path("msisensorpro_*.list")
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    """
+    msisensor-pro msi \\
+        -d $msisensorpro_scan \\
+        -n $bam_normal \\
+        -t $bam_tumor \\
+        -o $prefix \\
+        -b $task.cpus \\
+        $options.args
+
+    mv ${prefix}          msisensorpro_${prefix}.list
+    mv ${prefix}_dis      msisensorpro_${prefix}_dis.list
+    mv ${prefix}_germline msisensorpro_${prefix}_germline.list
+    mv ${prefix}_somatic  msisensorpro_${prefix}_somatic.list
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/msisensorpro/msi/meta.yml b/modules/nf-core/software/msisensorpro/msi/meta.yml
new file mode 100644
index 0000000000..e1d2220c67
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/msi/meta.yml
@@ -0,0 +1,58 @@
+name: msisensorpro_msi
+
+description: evaluate MSI using paired tumor-normal sequencing data
+keywords:
+  - microsatellite
+tools:
+  - msisensor:
+      description: MSIsensor-pro is an updated version of msisensor
+      homepage: https://github.com/xjtu-omics/msisensor-pro
+      documentation: None
+      tool_dev_url: None
+      doi: "doi.org/10.1016/j.gpb.2020.02.001"
+      licence: ['free for non-commercial use by academic, government, and non-profit/not-for-profit institutions']
+
+input:
+  - meta:
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+  - bam_normal:
+      type: file
+      description: |
+        BAM file from normal tissue
+  - bai_normal:
+      type: file
+      description: |
+          Index for the BAM file from normal tissue
+  - bam_tumor:
+      type: file
+      description: |
+          BAM file from tumor tissue
+  - bai_tumor:
+      type: file
+      description: |
+          Index for the BAM file from tumor tissue
+  - msisensor_scan:
+      type: file
+      description: |
+          Output file from msisensor-pro scan module
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - list:
+      type: file
+      description: |
+        msisensor-pro final report and associated files (dis, germline, somatic)
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@maxulysse"
diff --git a/modules/nf-core/software/msisensorpro/scan/functions.nf b/modules/nf-core/software/msisensorpro/scan/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/scan/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/msisensorpro/scan/main.nf b/modules/nf-core/software/msisensorpro/scan/main.nf
new file mode 100644
index 0000000000..0b346d91a0
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/scan/main.nf
@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MSISENSORPRO_SCAN {
+    tag "$fasta"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::msisensor-pro=1.1.a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/msisensor-pro:1.1.a--hb3646a4_0"
+    } else {
+        container "quay.io/biocontainers/msisensor-pro:1.1.a--hb3646a4_0"
+    }
+
+    input:
+    path fasta
+
+    output:
+    path "*.list",        emit: list
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${options.suffix}" : ""
+    """
+    msisensor-pro scan \\
+        -d $fasta \\
+        -o ${fasta.baseName}.list \\
+        $options.args
+
+    echo \$(msisensor-pro 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/msisensorpro/scan/meta.yml b/modules/nf-core/software/msisensorpro/scan/meta.yml
new file mode 100644
index 0000000000..5e9261aadb
--- /dev/null
+++ b/modules/nf-core/software/msisensorpro/scan/meta.yml
@@ -0,0 +1,32 @@
+name: msisensorpro_scan
+
+description: Scan the reference genome to get microsatellites information
+keywords:
+  - microsatellite
+tools:
+  - msisensor:
+      description: MSIsensor-pro is an updated version of msisensor
+      homepage: https://github.com/xjtu-omics/msisensor-pro
+      documentation: None
+      tool_dev_url: None
+      doi: "doi.org/10.1016/j.gpb.2020.02.001"
+      licence: ['free for non-commercial use by academic, government, and non-profit/not-for-profit institutions']
+
+input:
+  - fasta:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa,fasta}"
+
+output:
+  - list:
+      type: file
+      description: MSIsensor-pro scan output file of minisatellites
+      pattern: "*.list"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@maxulysse"
diff --git a/modules/nf-core/software/multiqc/functions.nf b/modules/nf-core/software/multiqc/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/multiqc/functions.nf
+++ b/modules/nf-core/software/multiqc/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/multiqc/main.nf b/modules/nf-core/software/multiqc/main.nf
index ff1175fcd0..da78080024 100644
--- a/modules/nf-core/software/multiqc/main.nf
+++ b/modules/nf-core/software/multiqc/main.nf
@@ -2,19 +2,19 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MULTIQC {
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
+    conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0"
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
     } else {
-        container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
+        container "quay.io/biocontainers/multiqc:1.10.1--py_0"
     }
 
     input:
diff --git a/modules/nf-core/software/multiqc/meta.yml b/modules/nf-core/software/multiqc/meta.yml
index 02f4b41586..532a8bb1ef 100644
--- a/modules/nf-core/software/multiqc/meta.yml
+++ b/modules/nf-core/software/multiqc/meta.yml
@@ -11,27 +11,6 @@ tools:
             It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
         homepage: https://multiqc.info/
         documentation: https://multiqc.info/docs/
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - multiqc_files:
         type: file
diff --git a/modules/nf-core/software/qualimap/bamqc/functions.nf b/modules/nf-core/software/qualimap/bamqc/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/qualimap/bamqc/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/qualimap/bamqc/main.nf b/modules/nf-core/software/qualimap/bamqc/main.nf
new file mode 100644
index 0000000000..463cde4cb7
--- /dev/null
+++ b/modules/nf-core/software/qualimap/bamqc/main.nf
@@ -0,0 +1,61 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process QUALIMAP_BAMQC {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    } else {
+        container "quay.io/biocontainers/qualimap:2.2.2d--1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path gff
+    val use_gff
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: results
+    path  "*.version.txt"             , emit: version
+
+    script:
+    def software   = getSoftwareName(task.process)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
+    def memory     = task.memory.toGiga() + "G"
+    def regions = use_gff ? "--gff $gff" : ''
+
+    def strandedness = 'non-strand-specific'
+    if (meta.strandedness == 'forward') {
+        strandedness = 'strand-specific-forward'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = 'strand-specific-reverse'
+    }
+    """
+    unset DISPLAY
+    mkdir tmp
+    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
+    qualimap \\
+        --java-mem-size=$memory \\
+        bamqc \\
+        $options.args \\
+        -bam $bam \\
+        $regions \\
+        -p $strandedness \\
+        $collect_pairs \\
+        -outdir $prefix \\
+        -nt $task.cpus
+
+    echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
+    """
+}
diff --git a/modules/nf-core/software/qualimap/bamqc/meta.yml b/modules/nf-core/software/qualimap/bamqc/meta.yml
new file mode 100644
index 0000000000..3c608f31a2
--- /dev/null
+++ b/modules/nf-core/software/qualimap/bamqc/meta.yml
@@ -0,0 +1,49 @@
+name: qualimap_bamqc
+description: Evaluate alignment data
+keywords:
+    - quality control
+    - qc
+    - bam
+tools:
+    - qualimap:
+        description: |
+          Qualimap 2 is a platform-independent application written in
+          Java and R that provides both a Graphical User Interface and
+          a command-line interface to facilitate the quality control of
+          alignment sequencing data and its derivatives like feature counts.
+        homepage: http://qualimap.bioinfo.cipf.es/
+        documentation: http://qualimap.conesalab.org/doc_html/index.html
+        doi: 10.1093/bioinformatics/bts503
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - gff:
+        type: file
+        description: Feature file with regions of interest
+        pattern: "*.{gff,gtf,bed}"
+    - use_gff:
+        type: boolean
+        description: Specifies if feature file should be used or not
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - results:
+        type: dir
+        description: Qualimap results dir
+        pattern: "*/*"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"
diff --git a/modules/nf-core/software/qualimap_bamqc.nf b/modules/nf-core/software/qualimap_bamqc.nf
deleted file mode 100644
index 055ad7cbf9..0000000000
--- a/modules/nf-core/software/qualimap_bamqc.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process QUALIMAP_BAMQC {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
-    } else {
-        container "quay.io/biocontainers/qualimap:2.2.2d--1"
-    }
-
-    input:
-         tuple val(meta), path(bam)
-         path(target_bed)
-
-     output:
-         path("${bam.baseName}") 
-
-     script:
-     use_bed = params.target_bed ? "-gff ${target_bed}" : ''
-     """
-     qualimap --java-mem-size=${task.memory.toGiga()}G \
-        bamqc \
-        -bam ${bam} \
-        --paint-chromosome-limits \
-        --genome-gc-distr HUMAN \
-        ${use_bed} \
-        -nt ${task.cpus} \
-        -skip-duplicated \
-        --skip-dup-mode 0 \
-        -outdir ${bam.baseName} \
-        -outformat HTML
-     """
-}
diff --git a/modules/nf-core/software/samtools/faidx/functions.nf b/modules/nf-core/software/samtools/faidx/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/samtools/faidx/functions.nf
+++ b/modules/nf-core/software/samtools/faidx/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/samtools/faidx/main.nf b/modules/nf-core/software/samtools/faidx/main.nf
index 85b7dd4dc1..6c023f1cd8 100644
--- a/modules/nf-core/software/samtools/faidx/main.nf
+++ b/modules/nf-core/software/samtools/faidx/main.nf
@@ -9,7 +9,7 @@ process SAMTOOLS_FAIDX {
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/samtools/index/functions.nf b/modules/nf-core/software/samtools/index/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/samtools/index/functions.nf
+++ b/modules/nf-core/software/samtools/index/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/samtools/index/main.nf b/modules/nf-core/software/samtools/index/main.nf
index 501e66c063..778e9384ea 100644
--- a/modules/nf-core/software/samtools/index/main.nf
+++ b/modules/nf-core/software/samtools/index/main.nf
@@ -1,13 +1,15 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_INDEX {
     tag "$meta.id"
+    label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -20,13 +22,14 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.bai"), emit: bai
+    tuple val(meta), path("*.bai"), optional:true, emit: bai
+    tuple val(meta), path("*.csi"), optional:true, emit: csi
     path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
-    samtools index $bam
+    samtools index $options.args $bam
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
 }
diff --git a/modules/nf-core/software/samtools/index/meta.yml b/modules/nf-core/software/samtools/index/meta.yml
index 089a83be02..5d076e3be5 100644
--- a/modules/nf-core/software/samtools/index/meta.yml
+++ b/modules/nf-core/software/samtools/index/meta.yml
@@ -14,27 +14,6 @@ tools:
         homepage: http://www.htslib.org/
         documentation: hhttp://www.htslib.org/doc/samtools.html
         doi: 10.1093/bioinformatics/btp352
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -55,6 +34,10 @@ output:
         type: file
         description: BAM/CRAM/SAM index file
         pattern: "*.{bai,crai,sai}"
+    - csi:
+        type: file
+        description: CSI index file
+        pattern: "*.{csi}"
     - version:
         type: file
         description: File containing software version
diff --git a/modules/nf-core/software/samtools/merge/functions.nf b/modules/nf-core/software/samtools/merge/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/samtools/merge/functions.nf
+++ b/modules/nf-core/software/samtools/merge/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/samtools/merge/main.nf b/modules/nf-core/software/samtools/merge/main.nf
index e60668db53..395b29e5d3 100644
--- a/modules/nf-core/software/samtools/merge/main.nf
+++ b/modules/nf-core/software/samtools/merge/main.nf
@@ -9,7 +9,7 @@ process SAMTOOLS_MERGE {
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -19,15 +19,15 @@ process SAMTOOLS_MERGE {
     }
 
     input:
-    tuple val(meta),path(bams)
+    tuple val(meta), path(bams)
 
     output:
     tuple val(meta), path("${prefix}.bam"), emit: merged_bam
-    path  "*.version.txt"                 , emit: version
+    path  "*.version.txt" ,                 emit: version
 
     script:
     def software = getSoftwareName(task.process)
-    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     samtools merge ${prefix}.bam $bams
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
diff --git a/modules/nf-core/software/samtools/merge/meta.yml b/modules/nf-core/software/samtools/merge/meta.yml
new file mode 100644
index 0000000000..9092f22e50
--- /dev/null
+++ b/modules/nf-core/software/samtools/merge/meta.yml
@@ -0,0 +1,44 @@
+name: samtools_merge
+description: Merge BAM file
+keywords:
+    - merge
+    - bam
+    - sam
+    - cram
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam,cram,sam}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - merged_bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@yuukiiwa "
+    - "@maxulysse"
diff --git a/modules/nf-core/software/samtools/stats/functions.nf b/modules/nf-core/software/samtools/stats/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/samtools/stats/functions.nf
+++ b/modules/nf-core/software/samtools/stats/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/samtools/stats/main.nf b/modules/nf-core/software/samtools/stats/main.nf
index 1863ac0a41..c307f9e8c3 100644
--- a/modules/nf-core/software/samtools/stats/main.nf
+++ b/modules/nf-core/software/samtools/stats/main.nf
@@ -1,19 +1,21 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_STATS {
     tag "$meta.id"
+    label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
     } else {
-        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
     }
 
     input:
diff --git a/modules/nf-core/software/samtools/stats/meta.yml b/modules/nf-core/software/samtools/stats/meta.yml
index b907df92c5..b549ff5c8f 100644
--- a/modules/nf-core/software/samtools/stats/meta.yml
+++ b/modules/nf-core/software/samtools/stats/meta.yml
@@ -15,27 +15,6 @@ tools:
         homepage: http://www.htslib.org/
         documentation: hhttp://www.htslib.org/doc/samtools.html
         doi: 10.1093/bioinformatics/btp352
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
diff --git a/modules/nf-core/software/strelka/germline.nf b/modules/nf-core/software/strelka/germline.nf
deleted file mode 100644
index 1b6f802912..0000000000
--- a/modules/nf-core/software/strelka/germline.nf
+++ /dev/null
@@ -1,54 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process STRELKA_GERMLINE {
-    tag "$meta.id"
-    label 'process_high'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
-    } else {
-        container "quay.io/biocontainers/strelka:2.9.10--0"
-    }
-
-    input:
-        tuple val(meta), path(bam), path(bai)
-        path fasta
-        path fai
-        tuple path(target_bed), path(target_bed_tbi)
-
-    output:
-        tuple val(meta), path("*_variants.vcf.gz"), path("*_variants.vcf.gz.tbi"), emit: vcf
-        tuple val(meta), path("*_genome.vcf.gz"), path("*_genome.vcf.gz.tbi"), emit: genome_vcf
-        path "*.version.txt", emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
-    def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
-    """
-    configureStrelkaGermlineWorkflow.py \
-        --bam ${bam} \
-        --referenceFasta ${fasta} \
-        ${options_strelka} \
-        --runDir strelka
-
-    python strelka/runWorkflow.py -m local -j ${task.cpus}
-
-    mv strelka/results/variants/genome.*.vcf.gz     ${prefix}_genome.vcf.gz
-    mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}_genome.vcf.gz.tbi
-    mv strelka/results/variants/variants.vcf.gz     ${prefix}_variants.vcf.gz
-    mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}_variants.vcf.gz.tbi
-
-    echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/strelka/germline/functions.nf b/modules/nf-core/software/strelka/germline/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/strelka/germline/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/strelka/germline/main.nf b/modules/nf-core/software/strelka/germline/main.nf
new file mode 100644
index 0000000000..16282cfad2
--- /dev/null
+++ b/modules/nf-core/software/strelka/germline/main.nf
@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process STRELKA_GERMLINE {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
+    } else {
+        container "quay.io/biocontainers/strelka:2.9.10--0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path  fasta
+    path  fai
+    path  target_bed
+
+    output:
+    tuple val(meta), path("*_variants.vcf.gz"), path("*_variants.vcf.gz.tbi"), emit: vcf
+    tuple val(meta), path("*_genome.vcf.gz"), path("*_genome.vcf.gz.tbi")    , emit: genome_vcf
+    path  "*.version.txt"                                                    , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
+    def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    """
+    configureStrelkaGermlineWorkflow.py \\
+        --bam $bam \\
+        --referenceFasta $fasta \\
+        $options_strelka \\
+        $options.args \\
+        --runDir strelka
+
+    python strelka/runWorkflow.py -m local -j $task.cpus
+
+    mv strelka/results/variants/genome.*.vcf.gz     ${prefix}_genome.vcf.gz
+    mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}_genome.vcf.gz.tbi
+    mv strelka/results/variants/variants.vcf.gz     ${prefix}_variants.vcf.gz
+    mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}_variants.vcf.gz.tbi
+
+    echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/strelka/germline/meta.yml b/modules/nf-core/software/strelka/germline/meta.yml
new file mode 100644
index 0000000000..1ad1885c9a
--- /dev/null
+++ b/modules/nf-core/software/strelka/germline/meta.yml
@@ -0,0 +1,55 @@
+name: strelka_germline
+description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
+keywords:
+  - variantcalling
+  - germline
+  - wgs
+  - vcf
+  - variants
+tools:
+  - strelka:
+      description: Strelka calls somatic and germline small variants from mapped sequencing reads
+      homepage: https://github.com/Illumina/strelka
+      documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
+      tool_dev_url: https://github.com/Illumina/strelka
+      doi: 10.1038/s41592-018-0051-x
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"
+  - target_bed:
+      type: file
+      description: An optional bed file
+      pattern: "*.{bed}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - vcf:
+      type: file
+      description: gzipped germline variant file and associated index file
+      pattern: "(*_variants.vcf.gz, *_variants.vcf.gz.tbi)"
+  - genome_vcf:
+      type: file
+      description: variant records and compressed non-variant blocks and associated index file
+      pattern: "(*_genome.vcf.gz, _genome.vcf.gz.tbi)"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@arontommi"
diff --git a/modules/nf-core/software/strelka/somatic.nf b/modules/nf-core/software/strelka/somatic.nf
deleted file mode 100644
index 4fd8c00f47..0000000000
--- a/modules/nf-core/software/strelka/somatic.nf
+++ /dev/null
@@ -1,110 +0,0 @@
-include { initOptions; saveFiles; getSoftwareName } from './../functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process STRELKA_SOMATIC {
-    tag "$meta.id"
-    label 'process_high'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
-    } else {
-        container "quay.io/biocontainers/strelka:2.9.10--0"
-    }
-
-    input:
-        tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor)
-        path fasta
-        path fai
-        tuple path(target_bed), path(target_bed_tbi)
-
-    output:
-        tuple val(meta), path("*_somatic_indels.vcf.gz"), path("*_somatic_indels.vcf.gz.tbi"), emit: indels_vcf
-        tuple val(meta), path("*_somatic_snvs.vcf.gz"), path("*_somatic_snvs.vcf.gz.tbi"),     emit: snvs_vcf
-        path "*.version.txt", emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
-    def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
-    """
-    configureStrelkaSomaticWorkflow.py \
-        --tumor ${bam_tumor} \
-        --normal ${bam_normal} \
-        --referenceFasta ${fasta} \
-        ${options_strelka} \
-        --runDir strelka
-
-    python strelka/runWorkflow.py -m local -j ${task.cpus}
-
-    mv strelka/results/variants/somatic.indels.vcf.gz     ${prefix}_somatic_indels.vcf.gz
-    mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}_somatic_indels.vcf.gz.tbi
-    mv strelka/results/variants/somatic.snvs.vcf.gz       ${prefix}_somatic_snvs.vcf.gz
-    mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   ${prefix}_somatic_snvs.vcf.gz.tbi
-
-    echo configureStrelkaSomaticWorkflow.py --version &> ${software}.version.txt #2>&1
-    """
-}
-
-process STRELKA_SOMATIC_BEST_PRACTICES {
-    tag "${meta.id}"
-    
-    label 'CPUS_MAX'
-    label 'MEMORY_MAX'
-    
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
-    } else {
-        container "quay.io/biocontainers/strelka:2.9.10--0"
-    }
-
-    input:
-        tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor), path(manta_csi), path(manta_csi_tbi)
-        path fasta
-        path fai
-        tuple path(target_bed), path(target_bed_tbi)
-
-    output:
-        tuple val(meta), path("*_somatic_indels.vcf.gz"), path("*_somatic_indels.vcf.gz.tbi"), emit: indels_vcf
-        tuple val(meta), path("*_somatic_snvs.vcf.gz"), path("*_somatic_snvs.vcf.gz.tbi"),     emit: snvs_vcf
-        path "*.version.txt", emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
-    def prefix   = ioptions.suffix ? "strelka_bp_${meta.id}${ioptions.suffix}" : "strelka_bp_${meta.id}"
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
-    """
-    configureStrelkaSomaticWorkflow.py \
-        --tumor ${bam_tumor} \
-        --normal ${bam_normal} \
-        --referenceFasta ${fasta} \
-        --indelCandidates ${manta_csi} \
-        ${options_strelka} \
-        --runDir strelka
-
-    python strelka/runWorkflow.py -m local -j ${task.cpus}
-
-    mv strelka/results/variants/somatic.indels.vcf.gz     ${prefix}_somatic_indels.vcf.gz
-    mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}_somatic_indels.vcf.gz.tbi
-    mv strelka/results/variants/somatic.snvs.vcf.gz       ${prefix}_somatic_snvs.vcf.gz
-    mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   ${prefix}_somatic_snvs.vcf.gz.tbi
-
-    echo configureStrelkaSomaticWorkflow.py --version &> ${software}.version.txt #2>&1
-    """
-}
\ No newline at end of file
diff --git a/modules/nf-core/software/strelka/somatic/functions.nf b/modules/nf-core/software/strelka/somatic/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/strelka/somatic/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/strelka/somatic/main.nf b/modules/nf-core/software/strelka/somatic/main.nf
new file mode 100644
index 0000000000..e57225fa39
--- /dev/null
+++ b/modules/nf-core/software/strelka/somatic/main.nf
@@ -0,0 +1,55 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process STRELKA_SOMATIC {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
+    } else {
+        container "quay.io/biocontainers/strelka:2.9.10--0"
+    }
+
+    input:
+    tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor)
+    path  fasta
+    path  fai
+    path  target_bed
+
+    output:
+    tuple val(meta), path("*_somatic_indels.vcf.gz"), path("*_somatic_indels.vcf.gz.tbi"), emit: indels_vcf
+    tuple val(meta), path("*_somatic_snvs.vcf.gz"), path("*_somatic_snvs.vcf.gz.tbi"),     emit: snvs_vcf
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
+    def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    """
+    configureStrelkaSomaticWorkflow.py \\
+        --tumor $bam_tumor \\
+        --normal $bam_normal \\
+        --referenceFasta $fasta \\
+        $options_strelka \\
+        $options.args \\
+        --runDir strelka
+
+    python strelka/runWorkflow.py -m local -j $task.cpus
+
+    mv strelka/results/variants/somatic.indels.vcf.gz     ${prefix}_somatic_indels.vcf.gz
+    mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}_somatic_indels.vcf.gz.tbi
+    mv strelka/results/variants/somatic.snvs.vcf.gz       ${prefix}_somatic_snvs.vcf.gz
+    mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   ${prefix}_somatic_snvs.vcf.gz.tbi
+
+    echo configureStrelkaSomaticWorkflow.py --version &> ${software}.version.txt #2>&1
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/strelka/somatic/meta.yml b/modules/nf-core/software/strelka/somatic/meta.yml
new file mode 100644
index 0000000000..5bf5878e1c
--- /dev/null
+++ b/modules/nf-core/software/strelka/somatic/meta.yml
@@ -0,0 +1,55 @@
+name: strelka_somatic
+description: Strelka2 is a fast and accurate small variant caller optimized for analysis of somatic variation
+keywords:
+  - variantcalling
+  - somatic
+  - wgs
+  - vcf
+  - variants
+tools:
+  - strelka:
+      description: Strelka calls somatic and germline small variants from mapped sequencing reads
+      homepage: https://github.com/Illumina/strelka
+      documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
+      tool_dev_url: https://github.com/Illumina/strelka
+      doi: 10.1038/s41592-018-0051-x
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"
+  - target_bed:
+      type: file
+      description: An optional bed file
+      pattern: "*.{bed}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - indels_vcf:
+      type: file
+      description: gzipped somatic indels file and associated index file
+      pattern: "(*_somatic_indels.vcf.gz, *_somatic_indels.vcf.gz.tbi)"
+  - snvs_vcf:
+      type: file
+      description: gzipped somatic snvs file and associated index file
+      pattern: "(*_somatic_snvs.vcf.gz, _somatic_snvs.vcf.gz.tbi)"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@arontommi"
diff --git a/modules/nf-core/software/strelka/somaticbp/functions.nf b/modules/nf-core/software/strelka/somaticbp/functions.nf
new file mode 100644
index 0000000000..da9da093d3
--- /dev/null
+++ b/modules/nf-core/software/strelka/somaticbp/functions.nf
@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/modules/nf-core/software/strelka/somaticbp/main.nf b/modules/nf-core/software/strelka/somaticbp/main.nf
new file mode 100644
index 0000000000..432481aebc
--- /dev/null
+++ b/modules/nf-core/software/strelka/somaticbp/main.nf
@@ -0,0 +1,56 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process STRELKA_SOMATIC_BEST_PRACTICES {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
+    } else {
+        container "quay.io/biocontainers/strelka:2.9.10--0"
+    }
+
+    input:
+    tuple val(meta), path(bam_normal), path(bai_normal), path(bam_tumor), path(bai_tumor), path(manta_csi), path(manta_csi_tbi)
+    path  fasta
+    path  fai
+    path  target_bed
+
+    output:
+    tuple val(meta), path("*_somatic_indels.vcf.gz"), path("*_somatic_indels.vcf.gz.tbi"), emit: indels_vcf
+    tuple val(meta), path("*_somatic_snvs.vcf.gz"), path("*_somatic_snvs.vcf.gz.tbi"),     emit: snvs_vcf
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
+    def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    """
+    configureStrelkaSomaticWorkflow.py \\
+        --tumor $bam_tumor \\
+        --normal $bam_normal \\
+        --referenceFasta $fasta \\
+        --indelCandidates $manta_csi \
+        $options_strelka \\
+        $options.args \\
+        --runDir strelka
+
+    python strelka/runWorkflow.py -m local -j $task.cpus
+
+    mv strelka/results/variants/somatic.indels.vcf.gz     ${prefix}_somatic_indels.vcf.gz
+    mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}_somatic_indels.vcf.gz.tbi
+    mv strelka/results/variants/somatic.snvs.vcf.gz       ${prefix}_somatic_snvs.vcf.gz
+    mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   ${prefix}_somatic_snvs.vcf.gz.tbi
+
+    echo configureStrelkaSomaticWorkflow.py --version &> ${software}.version.txt #2>&1
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/software/strelka/somaticbp/meta.yml b/modules/nf-core/software/strelka/somaticbp/meta.yml
new file mode 100644
index 0000000000..5bf5878e1c
--- /dev/null
+++ b/modules/nf-core/software/strelka/somaticbp/meta.yml
@@ -0,0 +1,55 @@
+name: strelka_somatic
+description: Strelka2 is a fast and accurate small variant caller optimized for analysis of somatic variation
+keywords:
+  - variantcalling
+  - somatic
+  - wgs
+  - vcf
+  - variants
+tools:
+  - strelka:
+      description: Strelka calls somatic and germline small variants from mapped sequencing reads
+      homepage: https://github.com/Illumina/strelka
+      documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
+      tool_dev_url: https://github.com/Illumina/strelka
+      doi: 10.1038/s41592-018-0051-x
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"
+  - target_bed:
+      type: file
+      description: An optional bed file
+      pattern: "*.{bed}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - indels_vcf:
+      type: file
+      description: gzipped somatic indels file and associated index file
+      pattern: "(*_somatic_indels.vcf.gz, *_somatic_indels.vcf.gz.tbi)"
+  - snvs_vcf:
+      type: file
+      description: gzipped somatic snvs file and associated index file
+      pattern: "(*_somatic_snvs.vcf.gz, _somatic_snvs.vcf.gz.tbi)"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@arontommi"
diff --git a/modules/nf-core/software/tabix/tabix/functions.nf b/modules/nf-core/software/tabix/tabix/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/tabix/tabix/functions.nf
+++ b/modules/nf-core/software/tabix/tabix/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/tabix/tabix/main.nf b/modules/nf-core/software/tabix/tabix/main.nf
index 0416a00ddb..da23f535bc 100644
--- a/modules/nf-core/software/tabix/tabix/main.nf
+++ b/modules/nf-core/software/tabix/tabix/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process TABIX_TABIX {
     tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/tabix/tabix/meta.yml b/modules/nf-core/software/tabix/tabix/meta.yml
index 8075184ade..f66270dba5 100644
--- a/modules/nf-core/software/tabix/tabix/meta.yml
+++ b/modules/nf-core/software/tabix/tabix/meta.yml
@@ -10,27 +10,6 @@ tools:
         homepage: https://www.htslib.org/doc/tabix.html
         documentation: https://www.htslib.org/doc/tabix.1.html
         doi: 10.1093/bioinformatics/btq671
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
diff --git a/modules/nf-core/software/trimgalore/functions.nf b/modules/nf-core/software/trimgalore/functions.nf
index d25eea86b3..da9da093d3 100644
--- a/modules/nf-core/software/trimgalore/functions.nf
+++ b/modules/nf-core/software/trimgalore/functions.nf
@@ -1,48 +1,57 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
+//
+//  Utility functions used in nf-core DSL2 module files
+//
 
-/*
- * Extract name of software tool from process name using $task.process
- */
+//
+// Extract name of software tool from process name using $task.process
+//
 def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
 def initOptions(Map args) {
     def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
     return options
 }
 
-/*
- * Tidy up and join elements of a list to return a path string
- */
+//
+// Tidy up and join elements of a list to return a path string
+//
 def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
     return paths.join('/')
 }
 
-/*
- * Function to save/publish module results
- */
+//
+// Function to save/publish module results
+//
 def saveFiles(Map args) {
     if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
+        def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
         }
         if (ioptions.publish_files instanceof Map) {
             for (ext in ioptions.publish_files) {
diff --git a/modules/nf-core/software/trimgalore/main.nf b/modules/nf-core/software/trimgalore/main.nf
index 79cc745625..44b36e7148 100644
--- a/modules/nf-core/software/trimgalore/main.nf
+++ b/modules/nf-core/software/trimgalore/main.nf
@@ -2,14 +2,14 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process TRIMGALORE {
     tag "$meta.id"
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/nf-core/software/trimgalore/meta.yml b/modules/nf-core/software/trimgalore/meta.yml
index 86ba5cd44a..735387076c 100644
--- a/modules/nf-core/software/trimgalore/meta.yml
+++ b/modules/nf-core/software/trimgalore/meta.yml
@@ -13,47 +13,6 @@ tools:
             MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
         homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
         documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
-    - clip_r1:
-        type: integer
-        description: |
-            Instructs Trim Galore to remove bp from the 5' end of read 1
-            (or single-end reads)
-    - clip_r2:
-        type: integer
-        description: |
-            Instructs Trim Galore to remove bp from the 5' end of read 2
-            (paired-end reads only)
-    - three_prime_clip_r1:
-        type: integer
-        description: |
-            Instructs Trim Galore to remove bp from the 3' end of read 1
-            AFTER adapter/quality trimming has been performed
-    - three_prime_clip_r2:
-        type: integer
-        description: |
-            Instructs Trim Galore to re move bp from the 3' end of read 2
-            AFTER adapter/quality trimming has been performed
 input:
     - meta:
         type: map
diff --git a/nextflow.config b/nextflow.config
index e2bcdffca5..4c2fffe4e9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,7 +22,7 @@ params {
 
   // Main options
   help = false
-  no_intervals = null // Intervals will be built from the fasta file
+  no_intervals = false // Intervals will be built from the fasta file
   nucleotides_per_second = 1000 // Default interval size
   sentieon = null // Not using Sentieon by default
   skip_qc = null // All QC tools are used
@@ -44,7 +44,7 @@ params {
   markdup_java_options = '"-Xms4000m -Xmx7g"' // Established values for markDuplicates memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details
   use_gatk_spark = false // GATK Spark implementation of their tools in local mode not used by default
   save_bam_mapped = null // Mapped BAMs not saved
-  skip_markduplicates = null // Do not skip markDuplicates by default
+  skip_markduplicates = false // Do not skip markDuplicates by default
 
   // Variant Calling
   ascat_ploidy = null // Use default value
@@ -52,7 +52,7 @@ params {
   cf_coeff = 0.05                    // default value for Control-FREEC
   cf_contamination = null            // by default not specified in Control-FREEC
   cf_contamination_adjustment = null // by default we are not using this in Control-FREEC
-  cf_ploidy = "2"                    // you can use 2,3,4
+  cf_ploidy = 2                      // you can use 2,3,4
   cf_window = null                   // by default we are not using this in Control-FREEC
   generate_gvcf = null // g.vcf are not produced by HaplotypeCaller by default
   no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available
@@ -76,6 +76,7 @@ params {
   vep_cache = null // No directory for VEP cache
 
   // Custom config
+  config_profile_name = null
   config_profile_contact = false
   config_profile_description = false
   config_profile_url = false
@@ -88,18 +89,14 @@ params {
   sequencing_center = null // No sequencing center to be written in BAM header in MapReads process
   multiqc_config = false
   monochrome_logs = false // Monochrome logs disabled
-  email = false // No default email
+  email = "" // No default email
   email_on_fail = false
   plaintext_email = false // Plaintext email disabled
   max_multiqc_email_size = 25.MB
   hostnames = false
-  config_profile_name = null
-  config_profile_description = false
-  config_profile_contact = false
-  config_profile_url = false
   validate_params = true
   show_hidden_params = false
-  schema_ignore_params = 'genomes,input_paths'
+  schema_ignore_params = 'genomes,modules'
   tracedir = "${params.outdir}/pipeline_info"
 
   // Modules
@@ -112,14 +109,8 @@ params {
   max_cpus = 16
   max_memory = 128.GB
   max_time = 240.h
-  single_cpu_mem = 7.GB
 }
 
-// Container slug
-// Stable releases should specify release tag (ie: `dsl2`)
-// Developmental code should specify dev
-// process.container = 'nfcore/sarek:dsl2'
-
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -141,69 +132,54 @@ try {
 }
 
 profiles {
-  conda {
+  charliecloud {
+    charliecloud.enabled = true
     docker.enabled = false
-    singularity.enabled = false
     podman.enabled = false
     shifter.enabled = false
-    charliecloud.enabled = false
+    singularity.enabled = false
+  }
+  conda {
     process.conda = "$projectDir/environment.yml"
+    charliecloud.enabled = false
+    docker.enabled = false
+    podman.enabled = false
+    shifter.enabled = false
+    singularity.enabled = false
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
-    singularity.enabled = false
+    docker.userEmulation = true
+    charliecloud.enabled = false
     podman.enabled = false
     shifter.enabled = false
-    charliecloud.enabled = false
-    // Avoid this error:
-    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
-    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
-    // once this is established and works well, nextflow might implement this behavior as new default.
-    docker.runOptions = '-u \$(id -u):\$(id -g)'
+    singularity.enabled = false
   }
-  singularity {
+  podman {
+    podman.enabled = true
+    charliecloud.enabled = false
     docker.enabled = false
-    singularity.enabled = true
-    podman.enabled = false
     shifter.enabled = false
-    charliecloud.enabled = false
+    singularity.enabled = false
+  }
+  singularity {
     singularity.autoMounts = true
     singularity.enabled = true
-    params.enable_conda = false
-  }
-  podman {
-    singularity.enabled = false
+    charliecloud.enabled = false
     docker.enabled = false
-    podman.enabled = true
+    podman.enabled = false
     shifter.enabled = false
-    charliecloud.enabled = false
   }
   shifter {
-    singularity.enabled = false
-    docker.enabled = false
-    podman.enabled = false
     shifter.enabled = true
     charliecloud.enabled = false
-  }
-  charliecloud {
-    singularity.enabled = false
     docker.enabled = false
     podman.enabled = false
-    shifter.enabled = false
-    charliecloud.enabled = true
+    singularity.enabled = false
   }
-  test                 { includeConfig 'conf/test.config' }
-  test_annotation      { includeConfig 'conf/test_annotation.config' }
-  test_haplotypecaller { includeConfig 'conf/test_germline_variantcalling.config' }
-  test_pair            { includeConfig 'conf/test_pair.config' }
-  test_split_fastq     { includeConfig 'conf/test_split_fastq.config' }
-  test_targeted        { includeConfig 'conf/test_targeted.config' }
-  test_tool            { includeConfig 'conf/test_tool.config' }
-  test_trimming        { includeConfig 'conf/test_trimming.config' }
-  test_umi_tso         { includeConfig 'conf/test_umi_tso.config' }
-  test_use_gatk_spark  { includeConfig 'conf/test_use_gatk_spark.config' }
-  test_umi_qiaseq      { includeConfig 'conf/test_umi_qiaseq.config' }
+  test      { includeConfig 'conf/test.config' }
+  test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load genomes.config or igenomes.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 81a46f457d..8dc16093a9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -26,18 +26,13 @@
                     "default": "mapping",
                     "fa_icon": "fas fa-play",
                     "description": "Starting step.",
-                    "help_text": "Only one step.\n> **NB** step can be specified with no concern for case, or the presence of `-` or `_`\n",
+                    "help_text": "Only one step",
                     "enum": [
                         "mapping",
                         "prepare_recalibration",
                         "recalibrate",
                         "variant_calling",
                         "annotate",
-                        "Control-FREEC",
-                        "ControlFREEC",
-                        "preparerecalibration",
-                        "variantCalling",
-                        "variantcalling",
                         "controlfreec"
                     ]
                 },
@@ -58,41 +53,26 @@
             "properties": {
                 "tools": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for variant calling and/or for annotation.",
-                    "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensor, Mutect2, Strelka\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n\n\n`DNAseq`, `DNAscope` and `TNscope` are only available with `--sentieon`\n\n> **NB** tools can be specified with no concern for case, or the presence of `-` or `_`\n",
+                    "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensorpro, Mutect2, Strelka\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n\n\n`DNAseq`, `DNAscope` and `TNscope` are only available with `--sentieon`\n\n> **NB** tools can be specified with no concern for case, or the presence of `-` or `_`\n",
                     "list": [
-                        "null",
-                        "ASCAT",
-                        "CNVkit",
-                        "ControlFREEC",
-                        "FreeBayes",
-                        "HaplotypeCaller",
-                        "Manta",
-                        "mpileup",
-                        "MSIsensor",
-                        "Mutect2",
-                        "Strelka",
-                        "TIDDIT",
-                        "snpEff",
-                        "VEP",
-                        "merge",
-                        "DNAseq",
-                        "DNAscope",
-                        "TNscope",
+                        null,
                         "ascat",
                         "cnvkit",
                         "controlfreec",
                         "freebayes",
                         "haplotypecaller",
                         "manta",
-                        "msisensor",
+                        "mpileup",
+                        "msisensorpro",
                         "mutect2",
                         "strelka",
                         "tiddit",
                         "snpeff",
                         "vep",
+                        "merge",
                         "dnaseq",
                         "dnascope",
                         "tnscope"
@@ -119,24 +99,23 @@
                 },
                 "skip_qc": {
                     "type": "string",
+                    "default": null,
                     "fa_icon": "fas fa-forward",
                     "description": "Disable specified QC and Reporting tools.",
                     "help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_qc BaseRecalibrator` is actually just not saving the reports.\n> **NB** `--skip_qc MarkDuplicates` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.\n> **NB** tools can be specified with no concern for case, or the presence of `-` or `_`",
                     "list": [
-                        "null",
-                        "all",
-                        "bamQC",
-                        "BaseRecalibrator",
-                        "BCFtools",
-                        "Documentation",
-                        "FastQC",
-                        "MarkDuplicates",
-                        "MultiQC",
+                        null,
+                        "bamqc",
+                        "baserecalibrator",
+                        "bcftools",
+                        "documentation",
+                        "fastqc",
+                        "markduplicates",
+                        "multiqc",
                         "samtools",
                         "vcftools",
                         "versions"
-                    ],
-                    "default": "null"
+                    ]
                 },
                 "target_bed": {
                     "type": "string",
@@ -163,6 +142,7 @@
                 },
                 "clip_r1": {
                     "type": "integer",
+                    "default": 0,
                     "fa_icon": "fas fa-cut",
                     "description": "Remove bp from the 5' end of read 1.",
                     "help_text": "This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end.\n",
@@ -170,6 +150,7 @@
                 },
                 "clip_r2": {
                     "type": "integer",
+                    "default": 0,
                     "description": "Remove bp from the 5' end of read 2.",
                     "help_text": "This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end.\n",
                     "fa_icon": "fas fa-cut",
@@ -177,6 +158,7 @@
                 },
                 "three_prime_clip_r1": {
                     "type": "integer",
+                    "default": 0,
                     "fa_icon": "fas fa-cut",
                     "description": "Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.",
                     "help_text": "This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.\n",
@@ -184,6 +166,7 @@
                 },
                 "three_prime_clip_r2": {
                     "type": "integer",
+                    "default": 0,
                     "fa_icon": "fas fa-cut",
                     "description": "Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.",
                     "help_text": "This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.\n",
@@ -191,6 +174,7 @@
                 },
                 "trim_nextseq": {
                     "type": "integer",
+                    "default": 0,
                     "fa_icon": "fas fa-cut",
                     "description": "Apply the --nextseq=X option, to trim based on quality after removing poly-G tails.",
                     "help_text": "This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.",
@@ -232,7 +216,7 @@
                 },
                 "markdup_java_options": {
                     "type": "string",
-                    "default": "-Xms4000m -Xmx7g",
+                    "default": "\"-Xms4000m -Xmx7g\"",
                     "fa_icon": "fas fa-memory",
                     "description": "Establish values for GATK MarkDuplicates memory consumption",
                     "help_text": "See [SciLifeLab/Sarek/pull/689](https://github.com/SciLifeLab/Sarek/pull/689)",
@@ -240,6 +224,7 @@
                 },
                 "use_gatk_spark": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-forward",
                     "description": "Enable usage of GATK Spark implementation"
                 },
@@ -250,6 +235,7 @@
                 },
                 "skip_markduplicates": {
                     "type": "boolean",
+                    "default": false,
                     "fa_icon": "fas fa-fast-forward",
                     "description": "Skip GATK MarkDuplicates",
                     "help_text": "This params will also save the mapped BAMS, to enable restart from step `prepare_recalibration`"
@@ -265,14 +251,14 @@
             "properties": {
                 "ascat_ploidy": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-wrench",
                     "description": "Overwrite ASCAT ploidy",
                     "help_text": "Requires that `--ascat_purity` is set"
                 },
                 "ascat_purity": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-wrench",
                     "description": "Overwrite ASCAT purity",
                     "help_text": "Requires that `--ascat_ploidy` is set"
@@ -290,13 +276,13 @@
                 },
                 "cf_contamination": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-wrench",
                     "description": "Design known contamination value for Control-FREEC"
                 },
                 "cf_ploidy": {
-                    "type": "string",
-                    "default": "2",
+                    "type": "integer",
+                    "default": 2,
                     "fa_icon": "fas fa-wrench",
                     "description": "Overwrite Control-FREEC ploidy"
                 },
@@ -343,14 +329,14 @@
                 },
                 "read_structure1": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-clipboard-list",
                     "description": "When processing UMIs, a read structure should always be provided for each of the fastq files.",
                     "help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the [fgbio documentation](https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures)"
                 },
                 "read_structure2": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-clipboard-list",
                     "description": "When processing UMIs, a read structure should always be provided for each of the fastq files.",
                     "help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the [fgbio documentation](https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures)"
@@ -366,17 +352,12 @@
             "properties": {
                 "annotate_tools": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-hammer",
                     "description": "Specify from which tools Sarek should look for VCF files to annotate",
                     "help_text": "Only for step `annotate`",
                     "list": [
-                        "null",
-                        "HaplotypeCaller",
-                        "Manta",
-                        "Mutect2",
-                        "Strelka",
-                        "TIDDIT",
+                        null,
                         "haplotypecaller",
                         "manta",
                         "mutect2",
@@ -387,6 +368,7 @@
                 },
                 "annotation_cache": {
                     "type": "boolean",
+                    "default": null,
                     "fa_icon": "fas fa-database",
                     "description": "Enable the use of cache for annotation",
                     "help_text": "And disable usage of Sarek snpeff and vep specific containers for annotation\n\nTo be used with `--snpeff_cache` and/or `--vep_cache`",
@@ -400,28 +382,28 @@
                 },
                 "cadd_indels": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-file",
                     "description": "Path to CADD InDels file.",
                     "hidden": true
                 },
                 "cadd_indels_tbi": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-file",
                     "description": "Path to CADD InDels index.",
                     "hidden": true
                 },
                 "cadd_wg_snvs": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-file",
                     "description": "Path to CADD SNVs file.",
                     "hidden": true
                 },
                 "cadd_wg_snvs_tbi": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-file",
                     "description": "Path to CADD SNVs index.",
                     "hidden": true
@@ -434,7 +416,7 @@
                 },
                 "snpeff_cache": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-database",
                     "description": "Path to snpEff cache",
                     "help_text": "To be used with `--annotation_cache`",
@@ -442,7 +424,7 @@
                 },
                 "vep_cache": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-database",
                     "description": "Path to VEP cache",
                     "help_text": "To be used with `--annotation_cache`",
@@ -682,7 +664,7 @@
                 },
                 "sequencing_center": {
                     "type": "string",
-                    "default": "null",
+                    "default": null,
                     "fa_icon": "fas fa-university",
                     "description": "Name of sequencing center to be displayed in BAM file",
                     "help_text": "It will be in the CN field",
@@ -710,13 +692,6 @@
                     "fa_icon": "fas fa-microchip",
                     "help_text": "Should be an integer e.g. `--cpus 7`"
                 },
-                "single_cpu_mem": {
-                    "type": "string",
-                    "default": "7 GB",
-                    "fa_icon": "fas fa-sd-card",
-                    "description": "Use to set memory for a single CPU.",
-                    "help_text": "Should be a string in the format integer-unit eg. `--single_cpu_mem '8.GB'`"
-                },
                 "max_cpus": {
                     "type": "integer",
                     "description": "Maximum number of CPUs that can be requested for any single job.",
diff --git a/scripts/filter_locifile.py b/scripts/filter_locifile.py
deleted file mode 100755
index 6f34f1437e..0000000000
--- a/scripts/filter_locifile.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#! /usr/bin/env python
-
-import sys, re, math, random
-
-#VCF file whould be downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp//release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
-
-vcffile = "ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf"
-
-outfile = "1000Genomes_20130502_SNP_maf0.3.vcf"
-of=open(outfile, 'w')
-for line in open(vcffile, 'r'):
-    line=line.strip()
-    if not line.startswith("#"):
-        pma=re.compile('MULTI_ALLELIC')
-        ma=pma.search(line)
-        if not (ma):
-            psnp=re.compile('VT=SNP')
-            snp=psnp.search(line)
-            if(snp):
-                info=line.split("\t")[7]
-                af_info=info.split(";")[1]
-                fq=float(af_info.split("=")[1])
-                if fq > 0.3:
-                    of.write("%s\t%s\n" %(line.split("\t")[0], line.split("\t")[1]))
-
diff --git a/subworkflow/local/mapping.nf b/subworkflow/local/mapping.nf
deleted file mode 100644
index 2b4da42f95..0000000000
--- a/subworkflow/local/mapping.nf
+++ /dev/null
@@ -1,186 +0,0 @@
-/*
-================================================================================
-                                     MAPPING
-================================================================================
-*/
-
-params.bwamem1_mem_options       = [:]
-params.bwamem1_mem_tumor_options = [:]
-params.bwamem2_mem_options       = [:]
-params.bwamem2_mem_tumor_options = [:]
-params.merge_bam_options         = [:]
-params.qualimap_bamqc_options    = [:]
-params.samtools_index_options    = [:]
-params.samtools_stats_options    = [:]
-
-include { BWA_MEM as BWAMEM1_MEM }       from '../../modules/nf-core/software/bwa/mem/main'        addParams(options: params.bwamem1_mem_options)
-include { BWA_MEM as BWAMEM1_MEM_T }     from '../../modules/nf-core/software/bwa/mem/main'        addParams(options: params.bwamem1_mem_tumor_options)
-include { BWAMEM2_MEM }                  from '../../modules/nf-core/software/bwamem2/mem/main.nf' addParams(options: params.bwamem2_mem_options)
-include { BWAMEM2_MEM as BWAMEM2_MEM_T } from '../../modules/nf-core/software/bwamem2/mem/main.nf' addParams(options: params.bwamem2_mem_tumor_options)
-include { SAMTOOLS_MERGE }               from '../../modules/nf-core/software/samtools/merge/main' addParams(options: params.merge_bam_options)
-include { QUALIMAP_BAMQC }               from '../../modules/nf-core/software/qualimap_bamqc'      addParams(options: params.qualimap_bamqc_options)
-include { SAMTOOLS_INDEX }               from '../../modules/nf-core/software/samtools/index/main' addParams(options: params.samtools_index_options)
-include { SAMTOOLS_STATS }               from '../../modules/nf-core/software/samtools/stats/main' addParams(options: params.samtools_stats_options)
-
-workflow MAPPING {
-    take:
-        skip_bamqc      // boolean: true/false
-        skip_samtools   // boolean: true/false
-        bwa             // channel: [mandatory] bwa
-        fai             // channel: [mandatory] fai
-        fasta           // channel: [mandatory] fasta
-        reads_input     // channel: [mandatory] reads_input
-        save_bam_mapped // boolean: true/false
-        step            //   value: [mandatory] starting step
-        target_bed      // channel: [optional]  target_bed
-
-    main:
-
-    bam_mapped_index = Channel.empty()
-    bam_reports      = Channel.empty()
-
-    reads_input.groupTuple(by: [0,1])
-            .branch{
-                normal: it[0].status == 0
-                tumor:  it[0].status == 1
-            }.set{ reads_input_status }
-
-    if (step == "mapping") {
-        bam_bwamem1 = Channel.empty()
-        bam_bwamem2 = Channel.empty()
-
-        if (params.aligner == "bwa-mem") {
-            BWAMEM1_MEM(reads_input_status.normal, bwa)
-            bam_bwamem1_n = BWAMEM1_MEM.out.bam
-
-            BWAMEM1_MEM_T(reads_input_status.tumor, bwa)
-            bam_bwamem1_t = BWAMEM1_MEM_T.out.bam
-
-            bam_bwamem1 = bam_bwamem1_n.mix(bam_bwamem1_t)
-        } else {
-            BWAMEM2_MEM(reads_input_status.normal, bwa)
-            bam_bwamem2_n = BWAMEM2_MEM.out.bam
-
-            BWAMEM2_MEM_T(reads_input_status.tumor, bwa)
-            bam_bwamem2_t = BWAMEM2_MEM_T.out.bam
-
-            bam_bwamem2 = bam_bwamem2_n.mix(bam_bwamem2_t)
-        }
-
-        bam_bwa = bam_bwamem1.mix(bam_bwamem2)
-
-        bam_bwa.map{ meta, bam ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            [patient, sample, gender, status, bam]
-        }.groupTuple(by: [0,1])
-            .branch{
-                single:   it[4].size() == 1
-                multiple: it[4].size() > 1
-            }.set{ bam_bwa_to_sort }
-
-        bam_bwa_single = bam_bwa_to_sort.single.map {
-            patient, sample, gender, status, bam ->
-
-            def meta = [:]
-            meta.patient = patient
-            meta.sample = sample
-            meta.gender = gender[0]
-            meta.status = status[0]
-            meta.id = sample
-
-            [meta, bam[0]]
-        }
-
-        bam_bwa_multiple = bam_bwa_to_sort.multiple.map {
-            patient, sample, gender, status, bam ->
-
-            def meta = [:]
-            meta.patient = patient
-            meta.sample = sample
-            meta.gender = gender[0]
-            meta.status = status[0]
-            meta.id = sample
-
-            [meta, bam]
-        }
-
-        // STEP 1.5: MERGING AND INDEXING BAM FROM MULTIPLE LANES 
-        
-        SAMTOOLS_MERGE(bam_bwa_multiple)
-        bam_mapped       = bam_bwa_single.mix(SAMTOOLS_MERGE.out.merged_bam)
-
-        SAMTOOLS_INDEX(bam_mapped)
-        bam_mapped_index = bam_mapped.join(SAMTOOLS_INDEX.out.bai)
-
-        qualimap_bamqc = Channel.empty()
-        samtools_stats = Channel.empty()
-
-        if (!skip_bamqc) {
-            QUALIMAP_BAMQC(bam_mapped, target_bed)
-            qualimap_bamqc = QUALIMAP_BAMQC.out
-        }
-
-        if (!skip_samtools) {
-            SAMTOOLS_STATS(bam_mapped_index)
-            samtools_stats = SAMTOOLS_STATS.out.stats
-        }
-
-        bam_reports = samtools_stats.mix(qualimap_bamqc)
-
-        if (save_bam_mapped) {
-            tsv_bam_mapped = bam_mapped.map { meta, bam -> [meta] }
-            // Creating TSV files to restart from this step
-            tsv_bam_mapped.collectFile(storeDir: "${params.outdir}/preprocessing/tsv") { meta ->
-                patient = meta.patient[0]
-                sample  = meta.sample[0]
-                gender  = meta.gender[0]
-                status  = meta.status[0]
-                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
-                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
-                ["mapped_${sample}.tsv", "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"]
-            }
-
-            tsv_bam_mapped.map { meta ->
-                patient = meta.patient[0]
-                sample  = meta.sample[0]
-                gender  = meta.gender[0]
-                status  = meta.status[0]
-                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
-                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
-                "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"
-            }.collectFile(name: "mapped.tsv", sort: true, storeDir: "${params.outdir}/preprocessing/tsv")
-        }
-        if (params.skip_markduplicates) {
-            tsv_bam_mapped = bam_mapped.map { meta, bam -> [meta] }
-            // Creating TSV files to restart from this step
-            tsv_bam_mapped.collectFile(storeDir: "${params.outdir}/preprocessing/tsv") { meta ->
-                patient = meta.patient[0]
-                sample  = meta.sample[0]
-                gender  = meta.gender[0]
-                status  = meta.status[0]
-                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
-                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
-                table = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.recal.table"
-                ["mapped_no_markduplicates_${sample}.tsv", "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\t${table}\n"]
-            }
-
-            tsv_bam_mapped.map { meta ->
-                patient = meta.patient[0]
-                sample  = meta.sample[0]
-                gender  = meta.gender[0]
-                status  = meta.status[0]
-                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
-                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
-                table = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.recal.table"
-                "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\t${table}\n"
-            }.collectFile(name: 'mapped_no_markduplicates.tsv', sort: true, storeDir: "${params.outdir}/preprocessing/tsv")
-        }
-    }
-
-    emit:
-        bam = bam_mapped_index
-        qc  = bam_reports
-}
diff --git a/subworkflow/local/markduplicates.nf b/subworkflow/local/markduplicates.nf
deleted file mode 100644
index 379cc3e321..0000000000
--- a/subworkflow/local/markduplicates.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
-================================================================================
-                                 MARKDUPLICATES
-================================================================================
-*/
-
-params.markduplicates_options = [:]
-
-include { GATK4_MARKDUPLICATES }       from '../../modules/nf-core/software/gatk4/markduplicates' addParams(options: params.markduplicates_options)
-include { GATK4_MARKDUPLICATES_SPARK } from '../../modules/nf-core/software/gatk4/markduplicates' addParams(options: params.markduplicates_options)
-
-workflow MARKDUPLICATES {
-    take:
-        bam_mapped // channel: [mandatory] bam_mapped
-        step       //   value: [mandatory] starting step
-
-    main:
-
-    bam_markduplicates    = bam_mapped
-    report_markduplicates = Channel.empty()
-
-    if (params.use_gatk_spark) {
-        GATK4_MARKDUPLICATES_SPARK(bam_mapped)
-        report_markduplicates = GATK4_MARKDUPLICATES_SPARK.out.report
-        bam_markduplicates    = GATK4_MARKDUPLICATES_SPARK.out.bam
-    } else {
-        GATK4_MARKDUPLICATES(bam_mapped)
-        report_markduplicates = GATK4_MARKDUPLICATES.out.report
-        bam_markduplicates    = GATK4_MARKDUPLICATES.out.bam
-    }
-
-    // Creating TSV files to restart from this step
-    bam_markduplicates.collectFile(storeDir: "${params.outdir}/preprocessing/tsv") { meta, bam, bai ->
-        patient = meta.patient
-        sample  = meta.sample
-        gender  = meta.gender
-        status  = meta.status
-        bam   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
-        bai   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
-        table = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.recal.table"
-        ["markduplicates_${sample}.tsv", "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\t${table}\n"]
-    }
-
-    bam_markduplicates.map { meta, bam, bai ->
-        patient = meta.patient
-        sample  = meta.sample
-        gender  = meta.gender
-        status  = meta.status
-        bam   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
-        bai   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
-        table = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.recal.table"
-        "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\t${table}\n"
-    }.collectFile(name: 'markduplicates.tsv', sort: true, storeDir: "${params.outdir}/preprocessing/tsv")
-
-    emit:
-        bam    = bam_markduplicates
-        report = report_markduplicates
-}
diff --git a/subworkflow/local/prepare_recalibration.nf b/subworkflow/local/prepare_recalibration.nf
deleted file mode 100644
index 7a92611338..0000000000
--- a/subworkflow/local/prepare_recalibration.nf
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
-================================================================================
-                              PREPARE RECALIBRATION
-================================================================================
-*/
-
-params.baserecalibrator_options  = [:]
-params.gatherbqsrreports_options = [:]
-
-include { GATK4_BASERECALIBRATOR  as BASERECALIBRATOR }  from '../../modules/nf-core/software/gatk4/baserecalibrator'  addParams(options: params.baserecalibrator_options)
-include { GATK4_GATHERBQSRREPORTS as GATHERBQSRREPORTS } from '../../modules/nf-core/software/gatk4/gatherbqsrreports' addParams(options: params.gatherbqsrreports_options)
-
-workflow PREPARE_RECALIBRATION {
-    take:
-        bam_markduplicates // channel: [mandatory] bam_markduplicates
-        dbsnp              // channel: [optional]  dbsnp
-        dbsnp_tbi          // channel: [optional]  dbsnp_tbi
-        dict               // channel: [mandatory] dict
-        fai                // channel: [mandatory] fai
-        fasta              // channel: [mandatory] fasta
-        intervals          // channel: [mandatory] intervals
-        known_indels       // channel: [optional]  known_indels
-        known_indels_tbi   // channel: [optional]  known_indels_tbi
-        step               //   value: [mandatory] starting step
-
-    main:
-
-    bam_baserecalibrator = bam_markduplicates.combine(intervals)
-    table_bqsr = Channel.empty()
-
-    if (step in ["mapping", "preparerecalibration"]) {
-
-        BASERECALIBRATOR(bam_baserecalibrator, dbsnp, dbsnp_tbi, dict, fai, fasta, known_indels, known_indels_tbi)
-        table_bqsr = BASERECALIBRATOR.out.report
-
-        // STEP 3.5: MERGING RECALIBRATION TABLES
-        if (!params.no_intervals) {
-            BASERECALIBRATOR.out.report.map{ meta, table ->
-                patient = meta.patient
-                sample  = meta.sample
-                gender  = meta.gender
-                status  = meta.status
-                [patient, sample, gender, status, table]
-            }.groupTuple(by: [0,1]).set{ recaltable }
-
-            recaltable = recaltable.map {
-                patient, sample, gender, status, recal ->
-
-                def meta = [:]
-                meta.patient = patient
-                meta.sample = sample
-                meta.gender = gender[0]
-                meta.status = status[0]
-                meta.id = sample
-
-                [meta, recal]
-            }
-
-            GATHERBQSRREPORTS(recaltable)
-            table_bqsr = GATHERBQSRREPORTS.out.table
-        }
-
-        // Creating TSV files to restart from this step
-        table_bqsr.collectFile(storeDir: "${params.outdir}/preprocessing/tsv") { meta, table ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            bam = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
-            bai = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
-            ["markduplicates_no_table_${sample}.tsv", "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"]
-        }
-
-        table_bqsr.map { meta, table ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            bam = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
-            bai = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
-            "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"
-        }.collectFile(name: 'markduplicates_no_table.tsv', sort: true, storeDir: "${params.outdir}/preprocessing/tsv")
-    }
-
-    emit:
-        table_bqsr = table_bqsr
-}
diff --git a/subworkflow/local/recalibrate.nf b/subworkflow/local/recalibrate.nf
deleted file mode 100644
index e470f46086..0000000000
--- a/subworkflow/local/recalibrate.nf
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
-================================================================================
-                                   RECALIBRATE
-================================================================================
-*/
-
-params.applybqsr_options      = [:]
-params.merge_bam_options      = [:]
-params.qualimap_bamqc_options = [:]
-params.samtools_index_options = [:]
-params.samtools_stats_options = [:]
-
-include { GATK4_APPLYBQSR as APPLYBQSR } from '../../modules/nf-core/software/gatk4/applybqsr'     addParams(options: params.applybqsr_options)
-include { QUALIMAP_BAMQC }               from '../../modules/nf-core/software/qualimap_bamqc'      addParams(options: params.qualimap_bamqc_options)
-include { SAMTOOLS_INDEX }               from '../../modules/nf-core/software/samtools/index/main' addParams(options: params.samtools_index_options)
-include { SAMTOOLS_MERGE }               from '../../modules/nf-core/software/samtools/merge/main' addParams(options: params.merge_bam_options)
-include { SAMTOOLS_STATS }               from '../../modules/nf-core/software/samtools/stats/main' addParams(options: params.samtools_stats_options)
-
-workflow RECALIBRATE {
-    take:
-        skip_bamqc     // boolean: true/false
-        skip_samtools  // boolean: true/false
-        bam            // channel: [mandatory] bam
-        dict           // channel: [mandatory] dict
-        fai            // channel: [mandatory] fai
-        fasta          // channel: [mandatory] fasta
-        intervals      // channel: [mandatory] intervals
-        step           //   value: [mandatory] starting step
-        target_bed     // channel: [optional]  target_bed
-
-    main:
-
-    bam_recalibrated_index = Channel.empty()
-    bam_recalibrated       = Channel.empty()
-    bam_reports            = Channel.empty()
-
-    if (step in ["mapping", "preparerecalibration", "recalibrate"]) {
-
-        bam_intervals = bam.combine(intervals)
-
-        APPLYBQSR(bam_intervals, dict, fasta, fai)
-
-        // STEP 4.5: MERGING AND INDEXING THE RECALIBRATED BAM FILES
-        if (params.no_intervals) {
-            bam_recalibrated = APPLYBQSR.out.bam
-        } else {
-            APPLYBQSR.out.bam.map{ meta, bam -> //, bai ->
-                patient = meta.patient
-                sample  = meta.sample
-                gender  = meta.gender
-                status  = meta.status
-                [patient, sample, gender, status, bam] //, bai]
-            }.groupTuple(by: [0,1]).set{ bam_recalibrated_interval }
-
-            bam_recalibrated_interval = bam_recalibrated_interval.map {
-                patient, sample, gender, status, bam -> //, bai ->
-
-                def meta = [:]
-                meta.patient = patient
-                meta.sample = sample
-                meta.gender = gender[0]
-                meta.status = status[0]
-                meta.id = sample
-
-                [meta, bam]
-            }
-
-            SAMTOOLS_MERGE(bam_recalibrated_interval)
-            bam_recalibrated = SAMTOOLS_MERGE.out.merged_bam
-        }
-
-        SAMTOOLS_INDEX(bam_recalibrated)
-        bam_recalibrated_index = bam_recalibrated.join(SAMTOOLS_INDEX.out.bai)
-
-        qualimap_bamqc = Channel.empty()
-        samtools_stats = Channel.empty()
-
-        if (!skip_bamqc) {
-            QUALIMAP_BAMQC(bam_recalibrated, target_bed)
-            qualimap_bamqc = QUALIMAP_BAMQC.out
-        }
-
-        if (!skip_samtools) {
-            SAMTOOLS_STATS(bam_recalibrated_index)
-            samtools_stats = SAMTOOLS_STATS.out.stats
-        }
-
-        bam_reports = samtools_stats.mix(qualimap_bamqc)
-
-        //TODO: set bam_recalibrated with all these steps
-        // // When using sentieon for mapping, Channel bam_recalibrated is bam_sentieon_recal
-        // if (params.sentieon && step == 'mapping') bam_recalibrated = bam_sentieon_recal
-
-        // // When no knownIndels for mapping, Channel bam_recalibrated is bam_duplicates_marked
-        // if (!params.known_indels && step == 'mapping') bam_recalibrated = bam_duplicates_marked
-
-        // // When starting with variant calling, Channel bam_recalibrated is input_sample
-        // if (step == 'variantcalling') bam_recalibrated = input_sample
-        // Creating TSV files to restart from this step
-        bam_recalibrated_index.collectFile(storeDir: "${params.outdir}/preprocessing/tsv") { meta, bam, bai ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            bam = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam"
-            bai = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam.bai"
-            ["recalibrated_${sample}.tsv", "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"]
-        }
-
-        bam_recalibrated_index.map { meta, bam, bai ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            bam = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam"
-            bai = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam.bai"
-            "${patient}\t${gender}\t${status}\t${sample}\t${bam}\t${bai}\n"
-        }.collectFile(name: 'recalibrated.tsv', sort: true, storeDir: "${params.outdir}/preprocessing/tsv")
-    }
-
-    emit:
-        bam = bam_recalibrated_index
-        qc  = bam_reports
-}
diff --git a/subworkflow/local/build_indices.nf b/subworkflows/local/build_indices.nf
similarity index 61%
rename from subworkflow/local/build_indices.nf
rename to subworkflows/local/build_indices.nf
index 28e56daf85..90c3f6ac2e 100644
--- a/subworkflow/local/build_indices.nf
+++ b/subworkflows/local/build_indices.nf
@@ -1,7 +1,7 @@
 /*
-================================================================================
-                                BUILDING INDICES
-================================================================================
+========================================================================================
+    BUILDING INDICES
+========================================================================================
 */
 
 params.build_intervals_options         = [:]
@@ -10,7 +10,7 @@ params.bwamem2_index_options           = [:]
 params.create_intervals_bed_options    = [:]
 params.gatk4_dict_options              = [:]
 params.index_target_bed_options        = [:]
-params.msisensor_scan_options          = [:]
+params.msisensorpro_scan_options       = [:]
 params.samtools_faidx_options          = [:]
 params.tabix_dbsnp_options             = [:]
 params.tabix_germline_resource_options = [:]
@@ -19,83 +19,85 @@ params.tabix_pon_options               = [:]
 
 // Initialize channels based on params or indices that were just built
 
-include { BUILD_INTERVALS }                              from '../../modules/local/build_intervals.nf'                                addParams(options: params.build_intervals_options)
-include { BWA_INDEX as BWAMEM1_INDEX }                   from '../../modules/nf-core/software/bwa/index/main.nf'                      addParams(options: params.bwa_index_options)
-include { BWAMEM2_INDEX }                                from '../../modules/nf-core/software/bwamem2/index/main.nf'                  addParams(options: params.bwamem2_index_options)
-include { CREATE_INTERVALS_BED }                         from '../../modules/local/create_intervals_bed.nf'                           addParams(options: params.create_intervals_bed_options)
-include { GATK4_CREATESEQUENCEDICTIONARY as GATK4_DICT } from '../../modules/nf-core/software/gatk4/createsequencedictionary/main.nf' addParams(options: params.gatk4_dict_options)
-include { TABIX_TABIX as TABIX_DBSNP }                   from '../../modules/nf-core/software/tabix/tabix/main.nf'                    addParams(options: params.tabix_dbsnp_options)
-include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE }       from '../../modules/nf-core/software/tabix/tabix/main.nf'                    addParams(options: params.tabix_germline_resource_options)
-include { TABIX_TABIX as TABIX_KNOWN_INDELS }            from '../../modules/nf-core/software/tabix/tabix/main.nf'                    addParams(options: params.tabix_known_indels_options)
-include { TABIX_TABIX as TABIX_PON }                     from '../../modules/nf-core/software/tabix/tabix/main.nf'                    addParams(options: params.tabix_pon_options)
-include { INDEX_TARGET_BED }                             from '../../modules/local/index_target_bed.nf'                               addParams(options: params.index_target_bed_options)
-include { MSISENSOR_SCAN }                               from '../../modules/nf-core/software/msisensor/scan.nf'                      addParams(options: params.msisensor_scan_options)
-include { SAMTOOLS_FAIDX }                               from '../../modules/nf-core/software/samtools/faidx/main.nf'                 addParams(options: params.samtools_faidx_options)
-
-workflow BUILD_INDICES{
+include { BUILD_INTERVALS }                              from '../../modules/local/build_intervals/main'                           addParams(options: params.build_intervals_options)
+include { BWA_INDEX as BWAMEM1_INDEX }                   from '../../modules/nf-core/software/bwa/index/main'                      addParams(options: params.bwa_index_options)
+include { BWAMEM2_INDEX }                                from '../../modules/nf-core/software/bwamem2/index/main'                  addParams(options: params.bwamem2_index_options)
+include { CREATE_INTERVALS_BED }                         from '../../modules/local/create_intervals_bed/main'                      addParams(options: params.create_intervals_bed_options)
+include { GATK4_CREATESEQUENCEDICTIONARY as GATK4_DICT } from '../../modules/nf-core/software/gatk4/createsequencedictionary/main' addParams(options: params.gatk4_dict_options)
+include { TABIX_TABIX as TABIX_DBSNP }                   from '../../modules/nf-core/software/tabix/tabix/main'                    addParams(options: params.tabix_dbsnp_options)
+include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE }       from '../../modules/nf-core/software/tabix/tabix/main'                    addParams(options: params.tabix_germline_resource_options)
+include { TABIX_TABIX as TABIX_KNOWN_INDELS }            from '../../modules/nf-core/software/tabix/tabix/main'                    addParams(options: params.tabix_known_indels_options)
+include { TABIX_TABIX as TABIX_PON }                     from '../../modules/nf-core/software/tabix/tabix/main'                    addParams(options: params.tabix_pon_options)
+include { INDEX_TARGET_BED }                             from '../../modules/local/index_target_bed/main'                          addParams(options: params.index_target_bed_options)
+include { MSISENSORPRO_SCAN }                            from '../../modules/nf-core/software/msisensorpro/scan/main'              addParams(options: params.msisensorpro_scan_options)
+include { SAMTOOLS_FAIDX }                               from '../../modules/nf-core/software/samtools/faidx/main'                 addParams(options: params.samtools_faidx_options)
+
+workflow BUILD_INDICES {
     take:
         dbsnp             // channel: [optional]  dbsnp
         fasta             // channel: [mandatory] fasta
+        fasta_fai         // channel: [optional]  fasta_fai
         germline_resource // channel: [optional]  germline_resource
         known_indels      // channel: [optional]  known_indels
         pon               // channel: [optional]  pon
-        step              //   value: [mandatory] starting step
         target_bed        // channel: [optionnal] target_bed
-        tools             //    list: [optional]  tools to run
 
     main:
 
     result_bwa  = Channel.empty()
     version_bwa = Channel.empty()
-    if (!(params.bwa) && 'mapping' in step)
+    if (!(params.bwa) && 'mapping' in params.step.toLowerCase())
         if (params.aligner == "bwa-mem") (result_bwa, version_bwa) = BWAMEM1_INDEX(fasta)
         else                             (result_bwa, version_bwa) = BWAMEM2_INDEX(fasta)
 
     result_dict = Channel.empty()
     version_dict = Channel.empty()
-    if (!(params.dict) && !('annotate' in step) && !('controlfreec' in step))
+    if (!(params.dict) && !('annotate' in params.step.toLowerCase()) && !('controlfreec' in params.step.toLowerCase()))
         (result_dict, version_dict) = GATK4_DICT(fasta)
 
     result_fai = Channel.empty()
+    if (fasta_fai) result_fai = fasta_fai
     version_fai = Channel.empty()
-    if (!(params.fasta_fai) && !('annotate' in step))
+    if (!(params.fasta_fai) && !('annotate' in params.step.toLowerCase()))
         (result_fai, version_fai) = SAMTOOLS_FAIDX(fasta)
 
     result_dbsnp_tbi = Channel.empty()
     version_dbsnp_tbi = Channel.empty()
-    if (!(params.dbsnp_index) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || 'tnscope' in tools))
+    if (!(params.dbsnp_index) && params.dbsnp && ('mapping' in params.step.toLowerCase() || 'prepare_recalibration' in params.step.toLowerCase() || 'controlfreec' in params.tools.toString().toLowerCase() || 'haplotypecaller' in params.tools.toString().toLowerCase() || 'mutect2' in params.tools.toString().toLowerCase() || 'tnscope' in params.tools.toString().toLowerCase()))
         (result_dbsnp_tbi, version_dbsnp_tbi) = TABIX_DBSNP([[id:"${dbsnp.fileName}"], dbsnp])
+    result_dbsnp_tbi = result_dbsnp_tbi.map {meta, tbi -> [tbi]}
 
     result_target_bed = Channel.empty()
     version_target_bed = Channel.empty()
-    if ((params.target_bed) && ('manta' in tools || 'strelka' in tools))
+    if ((params.target_bed) && ('manta' in params.tools.toString().toLowerCase() || 'strelka' in params.tools.toString().toLowerCase()))
         (result_target_bed, version_target_bed) = INDEX_TARGET_BED(target_bed)
 
     result_germline_resource_tbi = Channel.empty()
     version_germline_resource_tbi = Channel.empty()
-    if (!(params.germline_resource_index) && params.germline_resource && 'mutect2' in tools)
+    if (!(params.germline_resource_index) && params.germline_resource && 'mutect2' in params.tools.toString().toLowerCase())
         (result_germline_resource_tbi, version_germline_resource_tbi) = TABIX_GERMLINE_RESOURCE([[id:"${germline_resource.fileName}"], germline_resource])
 
     result_known_indels_tbi = Channel.empty()
     version_known_indels_tbi = Channel.empty()
-    if (!(params.known_indels_index) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step))
+    if (!(params.known_indels_index) && params.known_indels && ('mapping' in params.step.toLowerCase() || 'prepare_recalibration' in params.step.toLowerCase()))
         (result_known_indels_tbi, version_known_indels_tbi) = TABIX_KNOWN_INDELS([[id:"${known_indels.fileName}"], known_indels])
+    result_known_indels_tbi = result_known_indels_tbi.map {meta, tbi -> [tbi]}
 
-    result_msisensor_scan = Channel.empty()
-    version_msisensor_scan = Channel.empty()
-    if ('msisensor' in tools)
-        (result_msisensor_scan, version_msisensor_scan) = MSISENSOR_SCAN(fasta, result_fai)
+    result_msisensorpro_scan = Channel.empty()
+    version_msisensorpro_scan = Channel.empty()
+    if ('msisensorpro' in params.tools.toString().toLowerCase())
+        (result_msisensorpro_scan, version_msisensorpro_scan) = MSISENSORPRO_SCAN(fasta)
 
     result_pon_tbi = Channel.empty()
     version_pon_tbi = Channel.empty()
-    if (!(params.pon_index) && params.pon && ('tnscope' in tools || 'mutect2' in tools))
+    if (!(params.pon_index) && params.pon && ('tnscope' in params.tools.toString().toLowerCase() || 'mutect2' in params.tools.toString().toLowerCase()))
         (result_pon_tbi, version_pon_tbi) = TABIX_PON([[id:"${pon.fileName}"], pon])
 
     result_intervals = Channel.empty()
     if (params.no_intervals) {
         file("${params.outdir}/no_intervals.bed").text = "no_intervals\n"
         result_intervals = Channel.from(file("${params.outdir}/no_intervals.bed"))
-    } else if (!('annotate' in step) && !('controlfreec' in step))
+    } else if (!('annotate' in params.step.toLowerCase()) && !('controlfreec' in params.step.toLowerCase()))
         if (!params.intervals)
             result_intervals = CREATE_INTERVALS_BED(BUILD_INTERVALS(result_fai))
         else
@@ -129,7 +131,7 @@ workflow BUILD_INDICES{
         germline_resource_tbi = result_germline_resource_tbi
         intervals             = result_intervals
         known_indels_tbi      = result_known_indels_tbi
-        msisensor_scan        = result_msisensor_scan
+        msisensorpro_scan     = result_msisensorpro_scan
         pon_tbi               = result_pon_tbi
         target_bed_gz_tbi     = result_target_bed
 }
\ No newline at end of file
diff --git a/subworkflow/local/germline_variant_calling.nf b/subworkflows/local/germline_variant_calling.nf
similarity index 52%
rename from subworkflow/local/germline_variant_calling.nf
rename to subworkflows/local/germline_variant_calling.nf
index debeca7d04..c0151add27 100644
--- a/subworkflow/local/germline_variant_calling.nf
+++ b/subworkflows/local/germline_variant_calling.nf
@@ -1,7 +1,7 @@
 /*
-================================================================================
-                            GERMLINE VARIANT CALLING
-================================================================================
+========================================================================================
+    GERMLINE VARIANT CALLING
+========================================================================================
 */
 
 params.haplotypecaller_options        = [:]
@@ -10,11 +10,11 @@ params.concat_gvcf_options            = [:]
 params.concat_haplotypecaller_options = [:]
 params.strelka_options                = [:]
 
-include { GATK4_HAPLOTYPECALLER as HAPLOTYPECALLER } from '../../modules/nf-core/software/gatk4/haplotypecaller' addParams(options: params.haplotypecaller_options)
-include { GATK4_GENOTYPEGVCF as GENOTYPEGVCF }       from '../../modules/nf-core/software/gatk4/genotypegvcf'    addParams(options: params.genotypegvcf_options)
-include { CONCAT_VCF as CONCAT_GVCF }                from '../../modules/local/concat_vcf'                       addParams(options: params.concat_gvcf_options)
-include { CONCAT_VCF as CONCAT_HAPLOTYPECALLER }     from '../../modules/local/concat_vcf'                       addParams(options: params.concat_haplotypecaller_options)
-include { STRELKA_GERMLINE as STRELKA }              from '../../modules/nf-core/software/strelka/germline'      addParams(options: params.strelka_options)
+include { GATK4_HAPLOTYPECALLER as HAPLOTYPECALLER } from '../../modules/nf-core/software/gatk4/haplotypecaller/main' addParams(options: params.haplotypecaller_options)
+include { GATK4_GENOTYPEGVCF as GENOTYPEGVCF }       from '../../modules/nf-core/software/gatk4/genotypegvcf/main'    addParams(options: params.genotypegvcf_options)
+include { CONCAT_VCF as CONCAT_GVCF }                from '../../modules/local/concat_vcf/main'                       addParams(options: params.concat_gvcf_options)
+include { CONCAT_VCF as CONCAT_HAPLOTYPECALLER }     from '../../modules/local/concat_vcf/main'                       addParams(options: params.concat_haplotypecaller_options)
+include { STRELKA_GERMLINE as STRELKA }              from '../../modules/nf-core/software/strelka/germline/main'      addParams(options: params.strelka_options)
 
 workflow GERMLINE_VARIANT_CALLING {
     take:
@@ -27,7 +27,6 @@ workflow GERMLINE_VARIANT_CALLING {
         intervals         // channel: [mandatory] intervals
         target_bed        // channel: [optional]  target_bed
         target_bed_gz_tbi // channel: [optional]  target_bed_gz_tbi
-        tools             //   list:  [mandatory] list of tools
 
     main:
 
@@ -38,9 +37,16 @@ workflow GERMLINE_VARIANT_CALLING {
 
     if (intervals == []) no_intervals = true
 
-    if ('haplotypecaller' in tools) {
+    if ('haplotypecaller' in params.tools.toLowerCase()) {
+
         haplotypecaller_interval_bam = bam.combine(intervals)
 
+        bam.combine(intervals).map{ meta, bam, bai, intervals ->
+            new_meta = meta.clone()
+            new_meta.id = meta.sample + "_" + intervals.baseName
+            [new_meta, bam, bai, intervals]
+        }.set{haplotypecaller_interval_bam}
+
         // STEP GATK HAPLOTYPECALLER.1
 
         HAPLOTYPECALLER(
@@ -52,26 +58,13 @@ workflow GERMLINE_VARIANT_CALLING {
             fai,
             no_intervals)
 
-        haplotypecaller_gvcf = HAPLOTYPECALLER.out.gvcf.map{ meta, vcf ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            [ patient, sample, gender, status, vcf] 
-        }.groupTuple(by: [0,1])
-
-        haplotypecaller_gvcf = haplotypecaller_gvcf.map { patient, sample, gender, status, vcf ->
-            def meta = [:]
-            meta.patient = patient
-            meta.sample  = sample
-            meta.gender  = gender[0]
-            meta.status  = status[0]
-            meta.id      = meta.sample
-            [ meta, vcf ]
-        }
+        haplotypecaller_raw = HAPLOTYPECALLER.out.vcf.map{ meta,vcf ->
+            meta.id = meta.sample
+            [meta, vcf]
+        }.groupTuple()
 
         CONCAT_GVCF(
-            haplotypecaller_gvcf,
+            haplotypecaller_raw,
             fai,
             target_bed)
 
@@ -80,7 +73,7 @@ workflow GERMLINE_VARIANT_CALLING {
         // STEP GATK HAPLOTYPECALLER.2
 
         GENOTYPEGVCF(
-            HAPLOTYPECALLER.out.interval_gvcf,
+            HAPLOTYPECALLER.out.interval_vcf,
             dbsnp,
             dbsnp_tbi,
             dict,
@@ -88,33 +81,20 @@ workflow GERMLINE_VARIANT_CALLING {
             fai,
             no_intervals)
 
-        haplotypecaller_interval_vcf = GENOTYPEGVCF.out.vcf.map{ meta, vcf ->
-            patient = meta.patient
-            sample  = meta.sample
-            gender  = meta.gender
-            status  = meta.status
-            [ patient, sample, gender, status, vcf] 
-        }.groupTuple(by: [0,1])
-
-        haplotypecaller_interval_vcf = haplotypecaller_interval_vcf.map { patient, sample, gender, status, vcf ->
-            def meta = [:]
-            meta.patient = patient
-            meta.sample  = sample
-            meta.gender  = gender[0]
-            meta.status  = status[0]
-            meta.id      = meta.sample
-            [ meta, vcf ]
-        }
+        haplotypecaller_results = GENOTYPEGVCF.out.vcf.map{ meta, vcf ->
+            meta.id = meta.sample
+            [meta, vcf]
+        }.groupTuple()
 
         CONCAT_HAPLOTYPECALLER(
-            haplotypecaller_interval_vcf,
+            haplotypecaller_results,
             fai,
             target_bed)
-
-        haplotypecaller_vcf = CONCAT_GVCF.out.vcf
+        
+        haplotypecaller_vcf = CONCAT_HAPLOTYPECALLER.out.vcf
     }
 
-    if ('strelka' in tools) {
+    if ('strelka' in params.tools.toLowerCase()) {
         STRELKA(
             bam,
             fasta,
diff --git a/subworkflows/local/mapping_csv.nf b/subworkflows/local/mapping_csv.nf
new file mode 100644
index 0000000000..a622622914
--- /dev/null
+++ b/subworkflows/local/mapping_csv.nf
@@ -0,0 +1,42 @@
+/*
+========================================================================================
+    MAPPING_CSV
+========================================================================================
+*/
+
+workflow MAPPING_CSV {
+    take:
+        bam_mapped          // channel: [mandatory] meta, bam, bai
+        save_bam_mapped     // boolean: [mandatory] save_bam_mapped
+        skip_markduplicates // boolean: [mandatory] skip_markduplicates
+
+    main:
+        if (save_bam_mapped) {
+            csv_bam_mapped = bam_mapped.map { meta, bam, bai -> [meta] }
+            // Creating csv files to restart from this step
+            csv_bam_mapped.collectFile(storeDir: "${params.outdir}/preprocessing/csv") { meta ->
+                patient = meta.patient[0]
+                sample  = meta.sample[0]
+                gender  = meta.gender[0]
+                status  = meta.status[0]
+                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
+                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
+                ["mapped_${sample}.csv", "patient,gender,status,sample,bam,bai\n${patient},${gender},${status},${sample},${bam},${bai}\n"]
+            }.collectFile(name: "mapped.csv", keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/preprocessing/csv")
+        }
+
+        if (skip_markduplicates) {
+            csv_bam_mapped = bam_mapped.map { meta, bam, bai -> [meta] }
+            // Creating csv files to restart from this step
+            csv_bam_mapped.collectFile(storeDir: "${params.outdir}/preprocessing/csv") { meta ->
+                patient = meta.patient[0]
+                sample  = meta.sample[0]
+                gender  = meta.gender[0]
+                status  = meta.status[0]
+                bam   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam"
+                bai   = "${params.outdir}/preprocessing/${sample}/mapped/${sample}.bam.bai"
+                table = "${params.outdir}/preprocessing/${sample}/recal_table/${sample}.recal.table"
+                ["mapped_no_markduplicates_${sample}.csv", "patient,gender,status,sample,bam,bai,table\n${patient},${gender},${status},${sample},${bam},${bai},${table}\n"]
+            }.collectFile(name: 'mapped_no_markduplicates.csv', keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/preprocessing/csv")
+        }
+}
diff --git a/subworkflows/local/markduplicates_csv.nf b/subworkflows/local/markduplicates_csv.nf
new file mode 100644
index 0000000000..47b765f98d
--- /dev/null
+++ b/subworkflows/local/markduplicates_csv.nf
@@ -0,0 +1,23 @@
+/*
+========================================================================================
+    MARKDUPLICATES_CSV
+========================================================================================
+*/
+
+workflow MARKDUPLICATES_CSV {
+    take:
+        bam_markduplicates // channel: [mandatory] meta, bam, bai
+
+    main:
+        // Creating csv files to restart from this step
+        bam_markduplicates.collectFile(storeDir: "${params.outdir}/preprocessing/csv") { meta, bam, bai ->
+            patient = meta.patient
+            sample  = meta.sample
+            gender  = meta.gender
+            status  = meta.status
+            bam   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
+            bai   = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
+            table = "${params.outdir}/preprocessing/${sample}/recal_table/${sample}.recal.table"
+            ["markduplicates_${sample}.csv", "patient,gender,status,sample,bam,bai,table\n${patient},${gender},${status},${sample},${bam},${bai},${table}\n"]
+        }.collectFile(name: 'markduplicates.csv', keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/preprocessing/csv")
+}
diff --git a/subworkflow/local/pair_variant_calling.nf b/subworkflows/local/pair_variant_calling.nf
similarity index 75%
rename from subworkflow/local/pair_variant_calling.nf
rename to subworkflows/local/pair_variant_calling.nf
index 5654217909..ab14158f33 100644
--- a/subworkflow/local/pair_variant_calling.nf
+++ b/subworkflows/local/pair_variant_calling.nf
@@ -1,18 +1,18 @@
 /*
-================================================================================
-                             SOMATIC VARIANT CALLING
-================================================================================
+========================================================================================
+    SOMATIC VARIANT CALLING
+========================================================================================
 */
 
 params.manta_options                  = [:]
-params.msisensor_msi_options          = [:]
+params.msisensorpro_msi_options       = [:]
 params.strelka_options                = [:]
 params.strelka_bp_options             = [:]
 
-include { MANTA_SOMATIC as MANTA }                       from '../../modules/nf-core/software/manta/somatic'       addParams(options: params.manta_options)
-include { MSISENSOR_MSI }                                from '../../modules/nf-core/software/msisensor/msi'       addParams(options: params.msisensor_msi_options)
-include { STRELKA_SOMATIC as STRELKA }                   from '../../modules/nf-core/software/strelka/somatic'     addParams(options: params.strelka_options)
-include { STRELKA_SOMATIC_BEST_PRACTICES as STRELKA_BP } from '../../modules/nf-core/software/strelka/somatic'     addParams(options: params.strelka_bp_options)
+include { MANTA_SOMATIC as MANTA }                       from '../../modules/nf-core/software/manta/somatic/main'     addParams(options: params.manta_options)
+include { MSISENSORPRO_MSI }                             from '../../modules/nf-core/software/msisensorpro/msi/main'  addParams(options: params.msisensorpro_msi_options)
+include { STRELKA_SOMATIC as STRELKA }                   from '../../modules/nf-core/software/strelka/somatic/main'   addParams(options: params.strelka_options)
+include { STRELKA_SOMATIC_BEST_PRACTICES as STRELKA_BP } from '../../modules/nf-core/software/strelka/somaticbp/main' addParams(options: params.strelka_bp_options)
 
 workflow PAIR_VARIANT_CALLING {
     take:
@@ -23,10 +23,9 @@ workflow PAIR_VARIANT_CALLING {
         fai               // channel: [mandatory] fai
         fasta             // channel: [mandatory] fasta
         intervals         // channel: [mandatory] intervals
-        msisensor_scan    // channel: [optional]  msisensor_scan
+        msisensorpro_scan // channel: [optional]  msisensorpro_scan
         target_bed        // channel: [optional]  target_bed
         target_bed_gz_tbi // channel: [optional]  target_bed_gz_tbi
-        tools             //    list: [mandatory] list of tools
 
     main:
 
@@ -47,7 +46,7 @@ workflow PAIR_VARIANT_CALLING {
         meta.normal  = normal[1]
         meta.tumor   = tumor[1]
         meta.gender  = normal[2]
-        meta.id      = "${meta.tumor}_vs_${meta.normal}"
+        meta.id      = "${meta.tumor}_vs_${meta.normal}".toString()
 
         [meta, normal[4], normal[5], tumor[4], tumor[5]]
     }
@@ -55,7 +54,7 @@ workflow PAIR_VARIANT_CALLING {
     manta_vcf            = Channel.empty()
     strelka_vcf          = Channel.empty()
 
-    if ('manta' in tools) {
+    if ('manta' in params.tools.toLowerCase()) {
         MANTA(
             bam_pair,
             fasta,
@@ -70,7 +69,7 @@ workflow PAIR_VARIANT_CALLING {
 
         manta_vcf = manta_candidate_small_indels_vcf.mix(manta_candidate_sv_vcf,manta_diploid_sv_vcf,manta_somatic_sv_vcf)
 
-        if ('strelka' in tools) {
+        if ('strelka' in params.tools.toLowerCase()) {
             STRELKA_BP(
                 manta_csi_for_strelka_bp,
                 fasta,
@@ -84,13 +83,13 @@ workflow PAIR_VARIANT_CALLING {
         }
     }
 
-    if ('msisensor' in tools) {
-        MSISENSOR_MSI(
+    if ('msisensorpro' in params.tools.toLowerCase()) {
+        MSISENSORPRO_MSI(
             bam_pair,
-            msisensor_scan)
+            msisensorpro_scan)
     }
 
-    if ('strelka' in tools) {
+    if ('strelka' in params.tools.toLowerCase()) {
         STRELKA(
             bam_pair,
             fasta,
diff --git a/subworkflows/local/prepare_recalibration_csv.nf b/subworkflows/local/prepare_recalibration_csv.nf
new file mode 100644
index 0000000000..b6c4f177de
--- /dev/null
+++ b/subworkflows/local/prepare_recalibration_csv.nf
@@ -0,0 +1,22 @@
+/*
+========================================================================================
+    PREPARE_RECALIBRATION_CSV
+========================================================================================
+*/
+
+workflow PREPARE_RECALIBRATION_CSV {
+    take:
+        table_bqsr // channel: [mandatory] meta, table
+
+    main:
+        // Creating csv files to restart from this step
+        table_bqsr.collectFile(storeDir: "${params.outdir}/preprocessing/csv") { meta, table ->
+            patient = meta.patient
+            sample  = meta.sample
+            gender  = meta.gender
+            status  = meta.status
+            bam = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam"
+            bai = "${params.outdir}/preprocessing/${sample}/markduplicates/${sample}.md.bam.bai"
+            ["markduplicates_no_table_${sample}.csv", "patient,gender,status,sample,bam,bai\n${patient},${gender},${status},${sample},${bam},${bai}\n"]
+        }.collectFile(name: 'markduplicates_no_table.csv', keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/preprocessing/csv")
+}
diff --git a/subworkflows/local/recalibrate_csv.nf b/subworkflows/local/recalibrate_csv.nf
new file mode 100644
index 0000000000..ad50b1f8d3
--- /dev/null
+++ b/subworkflows/local/recalibrate_csv.nf
@@ -0,0 +1,22 @@
+/*
+========================================================================================
+    RECALIBRATE_CSV
+========================================================================================
+*/
+
+workflow RECALIBRATE_CSV {
+    take:
+        bam_recalibrated_index // channel: [mandatory] meta, bam, bai
+
+    main:
+        // Creating csv files to restart from this step
+        bam_recalibrated_index.collectFile(storeDir: "${params.outdir}/preprocessing/csv") { meta, bam, bai ->
+            patient = meta.patient
+            sample  = meta.sample
+            gender  = meta.gender
+            status  = meta.status
+            bam = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam"
+            bai = "${params.outdir}/preprocessing/${sample}/recalibrated/${sample}.recal.bam.bai"
+            ["recalibrated_${sample}.csv", "patient,gender,status,sample,bam,bai\n${patient},${gender},${status},${sample},${bam},${bai}\n"]
+        }.collectFile(name: 'recalibrated.csv', keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/preprocessing/csv")
+}
diff --git a/subworkflow/nf-core/fastqc_trimgalore.nf b/subworkflows/nf-core/fastqc_trimgalore.nf
similarity index 95%
rename from subworkflow/nf-core/fastqc_trimgalore.nf
rename to subworkflows/nf-core/fastqc_trimgalore.nf
index 87cac4e452..3a1a1cec09 100644
--- a/subworkflow/nf-core/fastqc_trimgalore.nf
+++ b/subworkflows/nf-core/fastqc_trimgalore.nf
@@ -11,18 +11,18 @@ include { TRIMGALORE       } from '../../modules/nf-core/software/trimgalore/mai
 workflow FASTQC_TRIMGALORE {
     take:
     reads         // channel: [ val(meta), [ reads ] ]
-    skip_fastqc   // boolean: true/false
+    // skip_fastqc   // boolean: true/false
     skip_trimming // boolean: true/false
 
     main:
     fastqc_html    = Channel.empty()
     fastqc_zip     = Channel.empty()
     fastqc_version = Channel.empty()
-    if (!skip_fastqc) {
+    // if (!skip_fastqc) {
         FASTQC ( reads ).html.set { fastqc_html }
         fastqc_zip     = FASTQC.out.zip
         fastqc_version = FASTQC.out.version
-    }
+    // }
 
     trim_reads = reads
     trim_html  = Channel.empty()
diff --git a/subworkflows/nf-core/mapping.nf b/subworkflows/nf-core/mapping.nf
new file mode 100644
index 0000000000..6be238afc5
--- /dev/null
+++ b/subworkflows/nf-core/mapping.nf
@@ -0,0 +1,106 @@
+/*
+========================================================================================
+    MAPPING
+========================================================================================
+*/
+
+params.bwamem1_mem_options       = [:]
+params.bwamem1_mem_tumor_options = [:]
+params.bwamem2_mem_options       = [:]
+params.bwamem2_mem_tumor_options = [:]
+params.merge_bam_options         = [:]
+params.qualimap_bamqc_options    = [:]
+params.samtools_index_options    = [:]
+params.samtools_stats_options    = [:]
+
+include { BWA_MEM as BWAMEM1_MEM }       from '../../modules/nf-core/software/bwa/mem/main'        addParams(options: params.bwamem1_mem_options)
+include { BWA_MEM as BWAMEM1_MEM_T }     from '../../modules/nf-core/software/bwa/mem/main'        addParams(options: params.bwamem1_mem_tumor_options)
+include { BWAMEM2_MEM }                  from '../../modules/nf-core/software/bwamem2/mem/main'    addParams(options: params.bwamem2_mem_options)
+include { BWAMEM2_MEM as BWAMEM2_MEM_T } from '../../modules/nf-core/software/bwamem2/mem/main'    addParams(options: params.bwamem2_mem_tumor_options)
+include { SAMTOOLS_MERGE }               from '../../modules/nf-core/software/samtools/merge/main' addParams(options: params.merge_bam_options)
+include { QUALIMAP_BAMQC }               from '../../modules/nf-core/software/qualimap/bamqc/main' addParams(options: params.qualimap_bamqc_options)
+include { SAMTOOLS_INDEX }               from '../../modules/nf-core/software/samtools/index/main' addParams(options: params.samtools_index_options)
+include { SAMTOOLS_STATS }               from '../../modules/nf-core/software/samtools/stats/main' addParams(options: params.samtools_stats_options)
+
+workflow MAPPING {
+    take:
+        skip_bamqc      // boolean: true/false
+        skip_samtools   // boolean: true/false
+        aligner         // string:  [mandatory] "bwa-mem" or "bwa-mem2"
+        bwa             // channel: [mandatory] bwa
+        fai             // channel: [mandatory] fai
+        fasta           // channel: [mandatory] fasta
+        reads_input     // channel: [mandatory] meta, reads_input
+        target_bed      // channel: [optional]  target_bed
+
+    main:
+
+    bam_mapped_index = Channel.empty()
+    bam_reports      = Channel.empty()
+
+    // If meta.status is 1, then sample is tumor
+    // else, (even is no meta.status exist) sample is normal
+    reads_input.branch{
+            tumor:  it[0].status == 1
+            normal: true
+        }.set{ reads_input_status }
+
+    bam_bwamem1 = Channel.empty()
+    bam_bwamem2 = Channel.empty()
+
+    if (aligner == "bwa-mem") {
+        BWAMEM1_MEM(reads_input_status.normal, bwa)
+        bam_bwamem1_n = BWAMEM1_MEM.out.bam
+
+        BWAMEM1_MEM_T(reads_input_status.tumor, bwa)
+        bam_bwamem1_t = BWAMEM1_MEM_T.out.bam
+
+        bam_bwamem1 = bam_bwamem1_n.mix(bam_bwamem1_t)
+    } else {
+        BWAMEM2_MEM(reads_input_status.normal, bwa)
+        bam_bwamem2_n = BWAMEM2_MEM.out.bam
+
+        BWAMEM2_MEM_T(reads_input_status.tumor, bwa)
+        bam_bwamem2_t = BWAMEM2_MEM_T.out.bam
+
+        bam_bwamem2 = bam_bwamem2_n.mix(bam_bwamem2_t)
+    }
+
+    bam_bwa = bam_bwamem1.mix(bam_bwamem2)
+
+    bam_bwa.map{ meta, bam ->
+        meta.remove('read_group')
+        meta.id = meta.sample
+        [meta, bam]
+    }.groupTuple().branch{
+        single:   it[1].size() == 1
+        multiple: it[1].size() > 1
+    }.set{ bam_bwa_to_sort }
+
+    // STEP 1.5: MERGING AND INDEXING BAM FROM MULTIPLE LANES 
+    
+    SAMTOOLS_MERGE(bam_bwa_to_sort.multiple)
+    bam_mapped = bam_bwa_to_sort.single.mix(SAMTOOLS_MERGE.out.merged_bam)
+
+    SAMTOOLS_INDEX(bam_mapped)
+    bam_mapped_index = bam_mapped.join(SAMTOOLS_INDEX.out.bai)
+
+    qualimap_bamqc = Channel.empty()
+    samtools_stats = Channel.empty()
+
+    if (!skip_bamqc) {
+        QUALIMAP_BAMQC(bam_mapped, target_bed, params.target_bed)
+        qualimap_bamqc = QUALIMAP_BAMQC.out
+    }
+
+    if (!skip_samtools) {
+        SAMTOOLS_STATS(bam_mapped_index)
+        samtools_stats = SAMTOOLS_STATS.out.stats
+    }
+
+    bam_reports = samtools_stats.mix(qualimap_bamqc)
+
+    emit:
+        bam = bam_mapped_index
+        qc  = bam_reports
+}
diff --git a/subworkflows/nf-core/markduplicates.nf b/subworkflows/nf-core/markduplicates.nf
new file mode 100644
index 0000000000..89f436b877
--- /dev/null
+++ b/subworkflows/nf-core/markduplicates.nf
@@ -0,0 +1,35 @@
+/*
+========================================================================================
+    MARKDUPLICATES
+========================================================================================
+*/
+
+params.markduplicates_options = [:]
+
+include { GATK4_MARKDUPLICATES }       from '../../modules/nf-core/software/gatk4/markduplicates/main'      addParams(options: params.markduplicates_options)
+include { GATK4_MARKDUPLICATES_SPARK } from '../../modules/nf-core/software/gatk4/markduplicatesspark/main' addParams(options: params.markduplicatesspark_options)
+
+workflow MARKDUPLICATES {
+    take:
+        bam_mapped     // channel: [mandatory] meta, bam, bai
+        use_gatk_spark //   value: [mandatory] use gatk spark
+        save_metrics   //   value: [mandatory] save metrics
+
+    main:
+
+    report_markduplicates = Channel.empty()
+
+    if (use_gatk_spark) {
+        GATK4_MARKDUPLICATES_SPARK(bam_mapped, save_metrics)
+        report_markduplicates = GATK4_MARKDUPLICATES_SPARK.out.metrics
+        bam_markduplicates    = GATK4_MARKDUPLICATES_SPARK.out.bam
+    } else {
+        GATK4_MARKDUPLICATES(bam_mapped, save_metrics)
+        report_markduplicates = GATK4_MARKDUPLICATES.out.metrics
+        bam_markduplicates    = GATK4_MARKDUPLICATES.out.bam
+    }
+
+    emit:
+        bam    = bam_markduplicates
+        report = report_markduplicates
+}
diff --git a/subworkflows/nf-core/prepare_recalibration.nf b/subworkflows/nf-core/prepare_recalibration.nf
new file mode 100644
index 0000000000..df53093470
--- /dev/null
+++ b/subworkflows/nf-core/prepare_recalibration.nf
@@ -0,0 +1,53 @@
+/*
+========================================================================================
+    PREPARE RECALIBRATION
+========================================================================================
+*/
+
+params.baserecalibrator_options  = [:]
+params.gatherbqsrreports_options = [:]
+
+include { GATK4_BASERECALIBRATOR  as BASERECALIBRATOR }  from '../../modules/nf-core/software/gatk4/baserecalibrator/main'  addParams(options: params.baserecalibrator_options)
+include { GATK4_GATHERBQSRREPORTS as GATHERBQSRREPORTS } from '../../modules/nf-core/software/gatk4/gatherbqsrreports/main' addParams(options: params.gatherbqsrreports_options)
+
+workflow PREPARE_RECALIBRATION {
+    take:
+        bam_markduplicates // channel: [mandatory] bam_markduplicates
+        dict               // channel: [mandatory] dict
+        fai                // channel: [mandatory] fai
+        fasta              // channel: [mandatory] fasta
+        intervals          // channel: [mandatory] intervals
+        known_sites        // channel: [optional]  known_sites
+        known_sites_tbi    // channel: [optional]  known_sites_tbi
+        no_intervals       //   value: [mandatory] no_intervals
+
+    main:
+
+    bam_markduplicates.combine(intervals).map{ meta, bam, bai, intervals ->
+        new_meta = meta.clone()
+        new_meta.id = meta.sample + "_" + intervals.baseName
+        [new_meta, bam, bai, intervals]
+    }.set{bam_markduplicates_intervals}
+
+    BASERECALIBRATOR(bam_markduplicates_intervals, fasta, fai, dict, known_sites, known_sites_tbi)
+
+    // STEP 3.5: MERGING RECALIBRATION TABLES
+    if (no_intervals) {
+        BASERECALIBRATOR.out.table.map { meta, table ->
+            meta.id = meta.sample
+            [meta, table]
+        }.set{table_bqsr}
+    } else {
+        BASERECALIBRATOR.out.table
+            .map{ meta, table ->
+            meta.id = meta.sample
+            [meta, table]
+        }.groupTuple().set{recaltable}
+
+        GATHERBQSRREPORTS(recaltable)
+        table_bqsr = GATHERBQSRREPORTS.out.table
+    }
+
+    emit:
+        table_bqsr = table_bqsr
+}
diff --git a/subworkflows/nf-core/recalibrate.nf b/subworkflows/nf-core/recalibrate.nf
new file mode 100644
index 0000000000..435f570b29
--- /dev/null
+++ b/subworkflows/nf-core/recalibrate.nf
@@ -0,0 +1,77 @@
+/*
+========================================================================================
+    RECALIBRATE
+========================================================================================
+*/
+
+params.applybqsr_options      = [:]
+params.merge_bam_options      = [:]
+params.qualimap_bamqc_options = [:]
+params.samtools_index_options = [:]
+params.samtools_stats_options = [:]
+
+include { GATK4_APPLYBQSR as APPLYBQSR } from '../../modules/nf-core/software/gatk4/applybqsr/main' addParams(options: params.applybqsr_options)
+include { QUALIMAP_BAMQC }               from '../../modules/nf-core/software/qualimap/bamqc/main'  addParams(options: params.qualimap_bamqc_options)
+include { SAMTOOLS_INDEX }               from '../../modules/nf-core/software/samtools/index/main'  addParams(options: params.samtools_index_options)
+include { SAMTOOLS_MERGE }               from '../../modules/nf-core/software/samtools/merge/main'  addParams(options: params.merge_bam_options)
+include { SAMTOOLS_STATS }               from '../../modules/nf-core/software/samtools/stats/main'  addParams(options: params.samtools_stats_options)
+
+workflow RECALIBRATE {
+    take:
+        skip_bamqc     // boolean: true/false
+        skip_samtools  // boolean: true/false
+        bam            // channel: [mandatory] bam
+        dict           // channel: [mandatory] dict
+        fai            // channel: [mandatory] fai
+        fasta          // channel: [mandatory] fasta
+        intervals      // channel: [mandatory] intervals
+        target_bed     // channel: [optional]  target_bed
+
+    main:
+
+    bam_recalibrated_index = Channel.empty()
+    bam_recalibrated       = Channel.empty()
+    bam_reports            = Channel.empty()
+
+    bam.combine(intervals).map{ meta, bam, bai, recal, intervals ->
+        new_meta = meta.clone()
+        new_meta.id = meta.sample + "_" + intervals.baseName
+        [new_meta, bam, bai, recal, intervals]
+    }.set{bam_intervals}
+
+    APPLYBQSR(bam_intervals, fasta, fai, dict)
+
+    // STEP 4.5: MERGING AND INDEXING THE RECALIBRATED BAM FILES
+    if (params.no_intervals) {
+        bam_recalibrated = APPLYBQSR.out.bam
+    } else {
+        APPLYBQSR.out.bam.map{ meta, bam ->
+            meta.id = meta.sample
+            [meta, bam]
+        }.groupTuple().set{bam_recalibrated_interval}
+
+        SAMTOOLS_MERGE(bam_recalibrated_interval)
+        bam_recalibrated = SAMTOOLS_MERGE.out.merged_bam
+
+        SAMTOOLS_INDEX(bam_recalibrated)
+        bam_recalibrated_index = bam_recalibrated.join(SAMTOOLS_INDEX.out.bai)
+
+        qualimap_bamqc = Channel.empty()
+        samtools_stats = Channel.empty()
+
+        if (!skip_bamqc) {
+            QUALIMAP_BAMQC(bam_recalibrated, target_bed, params.target_bed)
+            qualimap_bamqc = QUALIMAP_BAMQC.out
+        }
+
+        if (!skip_samtools) {
+            SAMTOOLS_STATS(bam_recalibrated_index)
+            samtools_stats = SAMTOOLS_STATS.out.stats
+        }
+        bam_reports = samtools_stats.mix(qualimap_bamqc)
+    }
+
+    emit:
+        bam = bam_recalibrated_index
+        qc  = bam_reports
+}
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index e224324ddf..e22feff405 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -31,5 +31,5 @@ includeConfig 'test_data.config'
 includeConfig '../../conf/modules.config'
 
 manifest {
-  nextflowVersion = '!>=20.11.0-edge'
+  nextflowVersion = '!>=21.04.0'
 }
diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml
index a180bfce88..b215cffcc6 100644
--- a/tests/config/pytest_software.yml
+++ b/tests/config/pytest_software.yml
@@ -1,4 +1,4 @@
 markduplicates:
-  - modules/nf-core/software/gatk4/markduplicates.nf
+  - modules/nf-core/software/gatk4/markduplicates/main.nf
   - subworkflow/local/markduplicates.nf
   - tests/subworkflow/local/markduplicates/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index e1b4617821..910379f589 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -4,7 +4,8 @@ def nf_core_modules_data = "https://raw.githubusercontent.com/nf-core/test-datas
 params {
     test_data {
         'nf-core' {
-            test_paired_end_sorted_bam = "${nf_core_modules_data}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam"
+            test_paired_end_sorted_bam = "${nf_core_modules_data}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
+            test_paired_end_sorted_bai = "${nf_core_modules_data}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
             genome_fasta               = "${nf_core_modules_data}/genomics/sarscov2/genome/genome.fasta"
             genome_sizes               = "${nf_core_modules_data}/genomics/sarscov2/genome/genome.sizes"
             'bed' {
diff --git a/tests/subworkflows/local/markduplicates/main.nf b/tests/subworkflows/local/markduplicates/main.nf
deleted file mode 100644
index fabd6cfbcf..0000000000
--- a/tests/subworkflows/local/markduplicates/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MARKDUPLICATES } from '../../../../subworkflow/local/markduplicates' addParams(
-    markduplicates_options:          modules['markduplicates']
-)
-
-workflow test_markduplicates {
-    input = [[ id: 'test' ],
-             [ file(params.test_data['nf-core']['test_paired_end_sorted_bam'], checkIfExists: true)]]
-
-    step = 'preparerecalibration'
-
-    MARKDUPLICATES ( input, step )
-}
diff --git a/tests/subworkflows/nf-core/markduplicates/main.nf b/tests/subworkflows/nf-core/markduplicates/main.nf
new file mode 100644
index 0000000000..feb130c696
--- /dev/null
+++ b/tests/subworkflows/nf-core/markduplicates/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+// Don't overwrite global params.modules, create a copy instead and use that within the main script.
+def modules = params.modules.clone()
+
+include { MARKDUPLICATES } from '../../../../subworkflows/nf-core/markduplicates' addParams(
+    markduplicates_options:      modules['markduplicates'],
+    markduplicatesspark_options: modules['markduplicatesspark']
+)
+
+workflow test_markduplicates {
+    input = [[id: 'test'],
+            [file(params.test_data['nf-core']['test_paired_end_sorted_bam'], checkIfExists: true)],
+            [file(params.test_data['nf-core']['test_paired_end_sorted_bai'], checkIfExists: true)]]
+
+    MARKDUPLICATES ( input, false, true )
+}
diff --git a/tests/subworkflows/local/markduplicates/test.yml b/tests/subworkflows/nf-core/markduplicates/test.yml
similarity index 51%
rename from tests/subworkflows/local/markduplicates/test.yml
rename to tests/subworkflows/nf-core/markduplicates/test.yml
index fdf9e9b228..427736fe2d 100644
--- a/tests/subworkflows/local/markduplicates/test.yml
+++ b/tests/subworkflows/nf-core/markduplicates/test.yml
@@ -1,9 +1,8 @@
 - name: subworkflow markduplicates
-  command: nextflow run ./tests/modules/local/subworkflows/markduplicates/ -entry test_markduplicates -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/markduplicates/ -entry test_markduplicates -c tests/config/nextflow.config
   tags:
     - markduplicates
     - gatk4
   files:
    - path: output/preprocessing/test/markduplicates/test.md.bam
    - path: output/preprocessing/test/markduplicates/test.md.bam.bai
-   - path: output/preprocessing/test/markduplicates/test.recal.table
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
index 6dffc1b3ff..437044bde4 100644
--- a/tests/test_aligner.yml
+++ b/tests/test_aligner.yml
@@ -1,36 +1,3 @@
-- name: Run bwa-mem
-  command: nextflow run main.nf -profile test,docker --aligner bwa-mem
-  tags:
-    - aligner
-    - bwa-mem
-  files:
-    - path: results/preprocessing/1234N/mapped/1234N.bam
-    - path: results/preprocessing/1234N/mapped/1234N.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
-
 - name: Run bwa-mem2
   command: nextflow run main.nf -profile test,docker --aligner bwa-mem2
   tags:
@@ -39,27 +6,22 @@
   files:
     - path: results/preprocessing/1234N/mapped/1234N.bam
     - path: results/preprocessing/1234N/mapped/1234N.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam.bai
+    - path: results/preprocessing/1234N/recal_table/1234N.recal.table
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam.bai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/reports/fastqc/1234N-1234N_M1
+    - path: results/reports/fastqc/1234N-1234N_M2
+    - path: results/reports/fastqc/1234N-1234N_M4
+    - path: results/reports/fastqc/1234N-1234N_M5
+    - path: results/reports/fastqc/1234N-1234N_M6
+    - path: results/reports/fastqc/1234N-1234N_M7
+    - path: results/reports/qualimap/1234N
+    - path: results/reports/samtools_stats/1234N/1234N.bam.stats
\ No newline at end of file
diff --git a/tests/test_default.yml b/tests/test_default.yml
index 645d6d82ae..61a5c744b9 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -6,29 +6,22 @@
   files:
     - path: results/preprocessing/1234N/mapped/1234N.bam
     - path: results/preprocessing/1234N/mapped/1234N.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam.bai
+    - path: results/preprocessing/1234N/recal_table/1234N.recal.table
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam.bai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/reports/fastqc/1234N-1234N_M1
+    - path: results/reports/fastqc/1234N-1234N_M2
+    - path: results/reports/fastqc/1234N-1234N_M4
+    - path: results/reports/fastqc/1234N-1234N_M5
+    - path: results/reports/fastqc/1234N-1234N_M6
+    - path: results/reports/fastqc/1234N-1234N_M7
     - path: results/reports/qualimap/1234N
-    - path: results/reports/samtools_stats/1234N/1234N.bam.stats
\ No newline at end of file
+    - path: results/reports/samtools_stats/1234N/1234N.bam.stats
diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
index 28291229b6..05aad7aa45 100644
--- a/tests/test_gatk_spark.yml
+++ b/tests/test_gatk_spark.yml
@@ -1,5 +1,5 @@
 - name: Run default pipeline with gatk_spark
-  command: nextflow run main.nf -profile test_use_gatk_spark,docker
+  command: nextflow run main.nf -profile test,use_gatk_spark,docker
   tags:
     - gatk4
     - gatk4_spark
@@ -7,29 +7,22 @@
   files:
     - path: results/preprocessing/1234N/mapped/1234N.bam
     - path: results/preprocessing/1234N/mapped/1234N.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam.bai
+    - path: results/preprocessing/1234N/recal_table/1234N.recal.table
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam.bai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/reports/fastqc/1234N-1234N_M1
+    - path: results/reports/fastqc/1234N-1234N_M2
+    - path: results/reports/fastqc/1234N-1234N_M4
+    - path: results/reports/fastqc/1234N-1234N_M5
+    - path: results/reports/fastqc/1234N-1234N_M6
+    - path: results/reports/fastqc/1234N-1234N_M7
     - path: results/reports/qualimap/1234N
     - path: results/reports/samtools_stats/1234N/1234N.bam.stats
\ No newline at end of file
diff --git a/tests/test_pair.yml b/tests/test_pair.yml
index 374e5a5d5e..1b6ce52740 100644
--- a/tests/test_pair.yml
+++ b/tests/test_pair.yml
@@ -1,53 +1,42 @@
 - name: Run default pipeline for tumor normal pair
-  command: nextflow run main.nf -profile test_pair,docker
+  command: nextflow run main.nf -profile test,pair,docker
   tags:
     - preprocessing
     - tumor_normal_pair
   files:
     - path: results/preprocessing/1234N/mapped/1234N.bam
     - path: results/preprocessing/1234N/mapped/1234N.bam.bai
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam.bai
+    - path: results/preprocessing/1234N/recal_table/1234N.recal.table
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam.bai
     - path: results/preprocessing/9876T/mapped/9876T.bam
     - path: results/preprocessing/9876T/mapped/9876T.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M1/9876T-9876T_M1_1_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M1/9876T-9876T_M1_1_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M1/9876T-9876T_M1_2_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M1/9876T-9876T_M1_2_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M2/9876T-9876T_M2_1_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M2/9876T-9876T_M2_1_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M2/9876T-9876T_M2_2_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M2/9876T-9876T_M2_2_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M4/9876T-9876T_M4_1_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M4/9876T-9876T_M4_1_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M4/9876T-9876T_M4_2_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M4/9876T-9876T_M4_2_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M5/9876T-9876T_M5_1_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M5/9876T-9876T_M5_1_fastqc.zip
-    - path: results/reports/fastqc/9876T-9876T_M5/9876T-9876T_M5_2_fastqc.html
-    - path: results/reports/fastqc/9876T-9876T_M5/9876T-9876T_M5_2_fastqc.zip
+    - path: results/preprocessing/9876T/markduplicates/9876T.md.bam
+    - path: results/preprocessing/9876T/markduplicates/9876T.md.bam.bai
+    - path: results/preprocessing/9876T/recal_table/9876T.recal.table
+    - path: results/preprocessing/9876T/recalibrated/9876T.recal.bam
+    - path: results/preprocessing/9876T/recalibrated/9876T.recal.bam.bai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_9876T.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_9876T.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/preprocessing/csv/recalibrated_9876T.csv
+    - path: results/reports/fastqc/1234N-1234N_M1
+    - path: results/reports/fastqc/1234N-1234N_M2
+    - path: results/reports/fastqc/1234N-1234N_M4
+    - path: results/reports/fastqc/1234N-1234N_M5
+    - path: results/reports/fastqc/1234N-1234N_M6
+    - path: results/reports/fastqc/1234N-1234N_M7
+    - path: results/reports/fastqc/9876T-9876T_M1
+    - path: results/reports/fastqc/9876T-9876T_M2
+    - path: results/reports/fastqc/9876T-9876T_M4
+    - path: results/reports/fastqc/9876T-9876T_M5
     - path: results/reports/qualimap/1234N
     - path: results/reports/qualimap/9876T
     - path: results/reports/samtools_stats/1234N/1234N.bam.stats
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
index 8ceb0ae552..203c691965 100644
--- a/tests/test_targeted.yml
+++ b/tests/test_targeted.yml
@@ -1,34 +1,27 @@
 - name: Run default pipeline with target bed
-  command: nextflow run main.nf -profile test_targeted,docker
+  command: nextflow run main.nf -profile test,targeted,docker
   tags:
     - preprocessing
     - targeted
   files:
     - path: results/preprocessing/1234N/mapped/1234N.bam
     - path: results/preprocessing/1234N/mapped/1234N.bam.bai
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M1/1234N-1234N_M1_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M2/1234N-1234N_M2_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M4/1234N-1234N_M4_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M5/1234N-1234N_M5_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M6/1234N-1234N_M6_2_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_1_fastqc.zip
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.html
-    - path: results/reports/fastqc/1234N-1234N_M7/1234N-1234N_M7_2_fastqc.zip
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam
+    - path: results/preprocessing/1234N/markduplicates/1234N.md.bam.bai
+    - path: results/preprocessing/1234N/recal_table/1234N.recal.table
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam
+    - path: results/preprocessing/1234N/recalibrated/1234N.recal.bam.bai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_1234N.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_1234N.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_1234N.csv
+    - path: results/reports/fastqc/1234N-1234N_M1
+    - path: results/reports/fastqc/1234N-1234N_M2
+    - path: results/reports/fastqc/1234N-1234N_M4
+    - path: results/reports/fastqc/1234N-1234N_M5
+    - path: results/reports/fastqc/1234N-1234N_M6
+    - path: results/reports/fastqc/1234N-1234N_M7
     - path: results/reports/qualimap/1234N
     - path: results/reports/samtools_stats/1234N/1234N.bam.stats
\ No newline at end of file
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index 1fe5b35cb6..e8a7af1c0a 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -1,5 +1,5 @@
 - name: Run variant calling for Haplotypecaller
-  command: nextflow run main.nf -profile test_tool,docker --tools Haplotypecaller
+  command: nextflow run main.nf -profile test,tool,docker --tools Haplotypecaller
   tags:
     - haplotypecaller
     - intervals
@@ -9,12 +9,8 @@
     - path: results/variant_calling/1234N/haplotypecaller/haplotypecaller_1234N.vcf.gz.tbi
     - path: results/variant_calling/1234N/haplotypecaller_gvcf/haplotypecaller_gvcf_1234N.vcf.gz
     - path: results/variant_calling/1234N/haplotypecaller_gvcf/haplotypecaller_gvcf_1234N.vcf.gz.tbi
-    - path: results/variant_calling/9876T/haplotypecaller/haplotypecaller_9876T.vcf.gz
-    - path: results/variant_calling/9876T/haplotypecaller/haplotypecaller_9876T.vcf.gz.tbi
-    - path: results/variant_calling/9876T/haplotypecaller_gvcf/haplotypecaller_gvcf_9876T.vcf.gz
-    - path: results/variant_calling/9876T/haplotypecaller_gvcf/haplotypecaller_gvcf_9876T.vcf.gz.tbi
 - name: Run variant calling for Haplotypecaller without intervals
-  command: nextflow run main.nf -profile test_tool,docker --tools Haplotypecaller --no_intervals
+  command: nextflow run main.nf -profile test,tool,docker --tools Haplotypecaller --no_intervals
   tags:
     - haplotypecaller
     - no_intervals
@@ -24,18 +20,13 @@
     - path: results/variant_calling/1234N/haplotypecaller/haplotypecaller_1234N.vcf.gz.tbi
     - path: results/variant_calling/1234N/haplotypecaller_gvcf/haplotypecaller_gvcf_1234N.vcf.gz
     - path: results/variant_calling/1234N/haplotypecaller_gvcf/haplotypecaller_gvcf_1234N.vcf.gz.tbi
-    - path: results/variant_calling/9876T/haplotypecaller/haplotypecaller_9876T.vcf.gz
-    - path: results/variant_calling/9876T/haplotypecaller/haplotypecaller_9876T.vcf.gz.tbi
-    - path: results/variant_calling/9876T/haplotypecaller_gvcf/haplotypecaller_gvcf_9876T.vcf.gz
-    - path: results/variant_calling/9876T/haplotypecaller_gvcf/haplotypecaller_gvcf_9876T.vcf.gz.tbi
-- name: Run variant calling for MSIsensor
-  command: nextflow run main.nf -profile test_tool,docker --tools MSIsensor
+- name: Run variant calling for MSIsensor-pro
+  command: nextflow run main.nf -profile test,tool_pair,docker --tools msisensorpro
   tags:
-    - intervals
-    - msisensor
+    - msisensorpro
     - variant_calling
   files:
-    - path: results/variant_calling/9876T_vs_1234N/msisensor/msisensor_9876T_vs_1234N_dis.list
-    - path: results/variant_calling/9876T_vs_1234N/msisensor/msisensor_9876T_vs_1234N_germline.list
-    - path: results/variant_calling/9876T_vs_1234N/msisensor/msisensor_9876T_vs_1234N.list
-    - path: results/variant_calling/9876T_vs_1234N/msisensor/msisensor_9876T_vs_1234N_somatic.list
\ No newline at end of file
+    - path: results/variant_calling/9876T_vs_1234N/msisensorpro/msisensorpro_9876T_vs_1234N_dis.list
+    - path: results/variant_calling/9876T_vs_1234N/msisensorpro/msisensorpro_9876T_vs_1234N_germline.list
+    - path: results/variant_calling/9876T_vs_1234N/msisensorpro/msisensorpro_9876T_vs_1234N.list
+    - path: results/variant_calling/9876T_vs_1234N/msisensorpro/msisensorpro_9876T_vs_1234N_somatic.list
\ No newline at end of file
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 7ee8f844d7..034651c59c 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -1,147 +1,105 @@
-////////////////////////////////////////////////////
-/* --          INCLUDE SAREK FUNCTIONS         -- */
-////////////////////////////////////////////////////
-
-include {
-    check_parameter_existence;
-    check_parameter_list;
-    define_anno_list;
-    define_skip_qc_list;
-    define_step_list;
-    define_tool_list;
-    extract_bam;
-    extract_fastq;
-    extract_fastq_from_dir;
-    extract_recal;
-    has_extension
-} from '../modules/local/functions'
-
-////////////////////////////////////////////////////
-/* --      SET UP CONFIGURATION VARIABLES      -- */
-////////////////////////////////////////////////////
-
-step_list = define_step_list()
-step = params.step ? params.step.toLowerCase().replaceAll('-', '').replaceAll('_', '') : ''
-
-if (step.contains(',')) exit 1, 'You can choose only one step, see --help for more information'
-if (!check_parameter_existence(step, step_list)) exit 1, "Unknown step ${step}, see --help for more information"
-
-tool_list = define_tool_list()
-tools = params.tools ? params.tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '').replaceAll('_', '')} : []
-if (step == 'controlfreec') tools = ['controlfreec']
-if (!check_parameter_list(tools, tool_list)) exit 1, 'Unknown tool(s), see --help for more information'
-
-skip_qc_list = define_skip_qc_list()
-skip_qc = params.skip_qc ? params.skip_qc == 'all' ? skip_qc_list : params.skip_qc.split(',').collect{it.trim().toLowerCase().replaceAll('-', '').replaceAll('_', '')} : []
-if (!check_parameter_list(skip_qc, skip_qc_list)) exit 1, 'Unknown QC tool(s), see --help for more information'
-
-anno_list = define_anno_list()
-annotate_tools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : []
-if (!check_parameter_list(annotate_tools,anno_list)) exit 1, 'Unknown tool(s) to annotate, see --help for more information'
-
-if (!(params.aligner in ['bwa-mem', 'bwa-mem2'])) exit 1, 'Unknown aligner, see --help for more information'
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
+def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+// Validate input parameters
+WorkflowSarek.initialise(params, log)
+
+// Check input path parameters to see if they exist
+checkPathParamList = [
+    params.ac_loci,
+    params.ac_loci_gc,
+    params.cadd_indels,
+    params.cadd_indels_tbi,
+    params.cadd_wg_snvs,
+    params.cadd_wg_snvs_tbi,
+    params.chr_dir,
+    params.chr_length,
+    params.dbsnp,
+    params.fasta,
+    params.fasta_fai,
+    params.germline_resource,
+    params.input,
+    params.known_indels,
+    params.mappability,
+    params.multiqc_config,
+    params.pon,
+    params.snpeff_cache,
+    params.target_bed,
+    params.vep_cache
+]
+
+for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+
+// Check mandatory parameters
+input_sample = Channel.empty()
 
-// // Check parameters
-if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them'
-if (params.cf_window && params.cf_coeff) exit 1, 'Please specify either --cf_window OR --cf_coeff, but not both of them'
-if (params.umi && !(params.read_structure1 && params.read_structure2)) exit 1, 'Please specify both --read_structure1 and --read_structure2, when using --umi'
+if (params.input) csv_file = file(params.input)
+else {
+    log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}"
+    switch (params.step.toLowerCase()) {
+        case 'mapping': break
+        case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
+        case 'recalibrate':           csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break
+        case 'variant_calling':       csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break
+        // case 'controlfreec':          csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
+        case 'annotate': break
+        default: exit 1, "Unknown step ${params.step}"
+    }   
+}
 
-// Handle input
-tsv_path = null
-if (params.input && (has_extension(params.input, "tsv") || has_extension(params.input, "vcf") || has_extension(params.input, "vcf.gz"))) tsv_path = params.input
-if (params.input && (has_extension(params.input, "vcf") || has_extension(params.input, "vcf.gz"))) step = "annotate"
+input_sample = extract_csv(csv_file)
 
 save_bam_mapped = params.skip_markduplicates ? true : params.save_bam_mapped ? true : false
 
-// If no input file specified, trying to get TSV files corresponding to step in the TSV directory
-// only for steps preparerecalibration, recalibrate, variantcalling and controlfreec
-if (!params.input && params.sentieon) {
-    switch (step) {
-        case 'mapping': break
-        case 'recalibrate': tsv_path = "${params.outdir}/preprocessing/tsv/sentieon_deduped.tsv"; break
-        case 'variantcalling': tsv_path = "${params.outdir}/preprocessing/tsv/sentieon_recalibrated.tsv"; break
-        case 'annotate': break
-        default: exit 1, "Unknown step ${step}"
-    }
-} else if (!params.input && !params.sentieon && !params.skip_markduplicates) {
-    switch (step) {
-        case 'mapping': break
-        case 'preparerecalibration': tsv_path = "${params.outdir}/preprocessing/tsv/markduplicates_no_table.tsv"; break
-        case 'recalibrate': tsv_path = "${params.outdir}/preprocessing/tsv/markduplicates.tsv"; break
-        case 'variantcalling': tsv_path = "${params.outdir}/preprocessing/tsv/recalibrated.tsv"; break
-        case 'controlfreec': tsv_path = "${params.outdir}/variant_calling/tsv/control-freec_mpileup.tsv"; break
-        case 'annotate': break
-        default: exit 1, "Unknown step ${step}"
-    }
-} else if (!params.input && !params.sentieon && params.skip_markduplicates) {
-    switch (step) {
-        case 'mapping': break
-        case 'preparerecalibration': tsv_path = "${params.outdir}/preprocessing/tsv/mapped.tsv"; break
-        case 'recalibrate': tsv_path = "${params.outdir}/preprocessing/tsv/mapped_no_markduplicates.tsv"; break
-        case 'variantcalling': tsv_path = "${params.outdir}/preprocessing/tsv/recalibrated.tsv"; break
-        case 'controlfreec': tsv_path = "${params.outdir}/variant_calling/tsv/control-freec_mpileup.tsv"; break
-        case 'annotate': break
-        default: exit 1, "Unknown step ${step}"
-    }
+// Save AWS IGenomes file containing annotation version
+def anno_readme = params.genomes[ params.genome ]?.readme
+if (anno_readme && file(anno_readme).exists()) {
+    file("${params.outdir}/genome/").mkdirs()
+    file(anno_readme).copyTo("${params.outdir}/genome/")
 }
 
-input_sample = Channel.empty()
-if (tsv_path) {
-    tsv_file = file(tsv_path)
-    switch (step) {
-        case 'mapping': input_sample = extract_fastq(tsv_file); break
-        case 'preparerecalibration': input_sample = extract_bam(tsv_file); break
-        case 'recalibrate': input_sample = extract_recal(tsv_file); break
-        case 'variantcalling': input_sample = extract_bam(tsv_file); break
-        case 'controlfreec': input_sample = extract_pileup(tsv_file); break
-        case 'annotate': break
-        default: exit 1, "Unknown step ${step}"
-    }
-} else if (params.input && !has_extension(params.input, "tsv")) {
-    log.info "No TSV file"
-    if (step != 'mapping') exit 1, 'No step other than "mapping" supports a directory as an input'
-    log.info "Reading ${params.input} directory"
-    log.warn "[nf-core/sarek] in ${params.input} directory, all fastqs are assuming to be from the same sample, which is assumed to be a germline one"
-    input_sample = extract_fastq_from_dir(params.input)
-    tsv_file = params.input  // used in the reports
-} else if (tsv_path && step == 'annotate') {
-    log.info "Annotating ${tsv_path}"
-} else if (step == 'annotate') {
-    log.info "Trying automatic annotation on files in the VariantCalling/ directory"
-} else exit 1, 'No sample were defined, see --help'
+// Stage dummy file to be used as an optional input where required
+ch_dummy_file = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)
 
 ////////////////////////////////////////////////////
 /* --  UPDATE MODULES OPTIONS BASED ON PARAMS  -- */
 ////////////////////////////////////////////////////
 
-modules = params.modules
-
-if (params.save_reference)      modules['build_intervals'].publish_files         = ['bed':'intervals']
-if (params.save_reference)      modules['bwa_index'].publish_files               = ['amb':'bwa', 'ann':'bwa', 'bwt':'bwa', 'pac':'bwa', 'sa':'bwa']
-if (params.save_reference)      modules['bwamem2_index'].publish_files           = ['0123':'bwamem2', 'amb':'bwamem2', 'ann':'bwamem2', 'bwt.2bit.64':'bwamem2', 'bwt.8bit.32':'bwamem2', 'pac':'bwamem2']
-if (params.save_reference)      modules['create_intervals_bed'].publish_files    = ['bed':'intervals']
-if (params.save_reference)      modules['dict'].publish_files                    = ['dict':'dict']
-if (params.save_reference)      modules['index_target_bed'].publish_files        = ['bed.gz':'target', 'bed.gz.tbi':'target']
-if (params.save_reference)      modules['msisensor_scan'].publish_files          = ['list':'msi']
-if (params.save_reference)      modules['samtools_faidx'].publish_files          = ['fai':'fai']
-if (params.save_reference)      modules['tabix_dbsnp'].publish_files             = ['vcf.gz.tbi':'dbsnp']
-if (params.save_reference)      modules['tabix_germline_resource'].publish_files = ['vcf.gz.tbi':'germline_resource']
-if (params.save_reference)      modules['tabix_known_indels'].publish_files      = ['vcf.gz.tbi':'known_indels']
-if (params.save_reference)      modules['tabix_pon'].publish_files               = ['vcf.gz.tbi':'pon']
-if (save_bam_mapped)            modules['samtools_index_mapping'].publish_files  = ['bam':'mapped', 'bai':'mapped']
-if (params.skip_markduplicates) modules['baserecalibrator'].publish_files        = ['recal.table':'mapped']
-if (params.skip_markduplicates) modules['gatherbqsrreports'].publish_files       = ['recal.table':'mapped']
+def modules = params.modules.clone()
+
+if (params.save_reference)       modules['build_intervals'].publish_files         = ['bed':'intervals']
+if (params.save_reference)       modules['bwa_index'].publish_files               = ['amb':'bwa', 'ann':'bwa', 'bwt':'bwa', 'pac':'bwa', 'sa':'bwa']
+if (params.save_reference)       modules['bwamem2_index'].publish_files           = ['0123':'bwamem2', 'amb':'bwamem2', 'ann':'bwamem2', 'bwt.2bit.64':'bwamem2', 'bwt.8bit.32':'bwamem2', 'pac':'bwamem2']
+if (params.save_reference)       modules['create_intervals_bed'].publish_files    = ['bed':'intervals']
+if (params.save_reference)       modules['dict'].publish_files                    = ['dict':'dict']
+if (params.save_reference)       modules['index_target_bed'].publish_files        = ['bed.gz':'target', 'bed.gz.tbi':'target']
+if (params.save_reference)       modules['msisensorpro_scan'].publish_files       = ['list':'msi']
+if (params.save_reference)       modules['samtools_faidx'].publish_files          = ['fai':'fai']
+if (params.save_reference)       modules['tabix_dbsnp'].publish_files             = ['vcf.gz.tbi':'dbsnp']
+if (params.save_reference)       modules['tabix_germline_resource'].publish_files = ['vcf.gz.tbi':'germline_resource']
+if (params.save_reference)       modules['tabix_known_indels'].publish_files      = ['vcf.gz.tbi':'known_indels']
+if (params.save_reference)       modules['tabix_pon'].publish_files               = ['vcf.gz.tbi':'pon']
+if (save_bam_mapped)             modules['samtools_index_mapping'].publish_files  = ['bam':'mapped', 'bai':'mapped']
+if (params.skip_markduplicates)  modules['baserecalibrator'].publish_files        = ['recal.table':'mapped']
+if (params.skip_markduplicates)  modules['gatherbqsrreports'].publish_files       = ['recal.table':'mapped']
+if (!params.skip_markduplicates) modules['baserecalibrator'].publish_files        = false
 
 // Initialize file channels based on params, defined in the params.genomes[params.genome] scope
-chr_dir           = params.chr_dir           ? file(params.chr_dir)           : []
-chr_length        = params.chr_length        ? file(params.chr_length)        : []
-dbsnp             = params.dbsnp             ? file(params.dbsnp)             : []
-fasta             = params.fasta             ? file(params.fasta)             : []
-germline_resource = params.germline_resource ? file(params.germline_resource) : []
-known_indels      = params.known_indels      ? file(params.known_indels)      : []
-loci              = params.ac_loci           ? file(params.ac_loci)           : []
-loci_gc           = params.ac_loci_gc        ? file(params.ac_loci_gc)        : []
-mappability       = params.mappability       ? file(params.mappability)       : []
+chr_dir           = params.chr_dir           ? file(params.chr_dir)           : ch_dummy_file
+chr_length        = params.chr_length        ? file(params.chr_length)        : ch_dummy_file
+dbsnp             = params.dbsnp             ? file(params.dbsnp)             : ch_dummy_file
+fasta             = params.fasta             ? file(params.fasta)             : ch_dummy_file
+fasta_fai         = params.fasta_fai         ? file(params.fasta_fai)         : ch_dummy_file
+germline_resource = params.germline_resource ? file(params.germline_resource) : ch_dummy_file
+known_indels      = params.known_indels      ? file(params.known_indels)      : ch_dummy_file
+loci              = params.ac_loci           ? file(params.ac_loci)           : ch_dummy_file
+loci_gc           = params.ac_loci_gc        ? file(params.ac_loci_gc)        : ch_dummy_file
+mappability       = params.mappability       ? file(params.mappability)       : ch_dummy_file
 
 // Initialize value channels based on params, defined in the params.genomes[params.genome] scope
 snpeff_db         = params.snpeff_db         ?: Channel.empty()
@@ -149,41 +107,38 @@ snpeff_species    = params.species           ?: Channel.empty()
 vep_cache_version = params.vep_cache_version ?: Channel.empty()
 
 // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope
-cadd_indels       = params.cadd_indels       ? file(params.cadd_indels)      : []
-cadd_indels_tbi   = params.cadd_indels_tbi   ? file(params.cadd_indels_tbi)  : []
-cadd_wg_snvs      = params.cadd_wg_snvs      ? file(params.cadd_wg_snvs)     : []
-cadd_wg_snvs_tbi  = params.cadd_wg_snvs_tbi  ? file(params.cadd_wg_snvs_tbi) : []
-pon               = params.pon               ? file(params.pon)              : []
-snpeff_cache      = params.snpeff_cache      ? file(params.snpeff_cache)     : []
-target_bed        = params.target_bed        ? file(params.target_bed)       : []
-vep_cache         = params.vep_cache         ? file(params.vep_cache)        : []
+cadd_indels       = params.cadd_indels       ? file(params.cadd_indels)      : ch_dummy_file
+cadd_indels_tbi   = params.cadd_indels_tbi   ? file(params.cadd_indels_tbi)  : ch_dummy_file
+cadd_wg_snvs      = params.cadd_wg_snvs      ? file(params.cadd_wg_snvs)     : ch_dummy_file
+cadd_wg_snvs_tbi  = params.cadd_wg_snvs_tbi  ? file(params.cadd_wg_snvs_tbi) : ch_dummy_file
+pon               = params.pon               ? file(params.pon)              : ch_dummy_file
+snpeff_cache      = params.snpeff_cache      ? file(params.snpeff_cache)     : ch_dummy_file
+target_bed        = params.target_bed        ? file(params.target_bed)       : ch_dummy_file
+vep_cache         = params.vep_cache         ? file(params.vep_cache)        : ch_dummy_file
 
 // Initialize value channels based on params, not defined within the params.genomes[params.genome] scope
 read_structure1   = params.read_structure1   ?: Channel.empty()
 read_structure2   = params.read_structure2   ?: Channel.empty()
 
-if ('mutect2' in tools && !(params.pon)) log.warn "[nf-core/sarek] Mutect2 was requested, but as no panel of normals were given, results will not be optimal"
-if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works if Sentieon is available where nf-core/sarek is run"
-
 ////////////////////////////////////////////////////
 /* --        INCLUDE LOCAL SUBWORKFLOWS        -- */
 ////////////////////////////////////////////////////
 
-include { BUILD_INDICES } from '../subworkflow/local/build_indices' addParams(
+include { BUILD_INDICES } from '../subworkflows/local/build_indices' addParams(
     build_intervals_options:         modules['build_intervals'],
     bwa_index_options:               modules['bwa_index'],
     bwamem2_index_options:           modules['bwamem2_index'],
     create_intervals_bed_options:    modules['create_intervals_bed'],
-    gatk_dict_options:               modules['dict'],
+    gatk4_dict_options:              modules['dict'],
     index_target_bed_options:        modules['index_target_bed'],
-    msisensor_scan_options:          modules['msisensor_scan'],
+    msisensorpro_scan_options:       modules['msisensorpro_scan'],
     samtools_faidx_options:          modules['samtools_faidx'],
     tabix_dbsnp_options:             modules['tabix_dbsnp'],
     tabix_germline_resource_options: modules['tabix_germline_resource'],
     tabix_known_indels_options:      modules['tabix_known_indels'],
     tabix_pon_options:               modules['tabix_pon']
 )
-include { MAPPING } from '../subworkflow/local/mapping' addParams(
+include { MAPPING } from '../subworkflows/nf-core/mapping' addParams(
     bwamem1_mem_options:             modules['bwa_mem1_mem'],
     bwamem1_mem_tumor_options:       modules['bwa_mem1_mem_tumor'],
     bwamem2_mem_options:             modules['bwa_mem2_mem'],
@@ -193,32 +148,37 @@ include { MAPPING } from '../subworkflow/local/mapping' addParams(
     samtools_index_options:          modules['samtools_index_mapping'],
     samtools_stats_options:          modules['samtools_stats_mapping']
 )
-include { MARKDUPLICATES } from '../subworkflow/local/markduplicates' addParams(
-    markduplicates_options:          modules['markduplicates']
+include { MAPPING_CSV } from '../subworkflows/local/mapping_csv'
+include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' addParams(
+    markduplicates_options:          modules['markduplicates'],
+    markduplicatesspark_options:     modules['markduplicatesspark']
 )
-include { PREPARE_RECALIBRATION } from '../subworkflow/local/prepare_recalibration' addParams(
+include { MARKDUPLICATES_CSV } from '../subworkflows/local/markduplicates_csv'
+include { PREPARE_RECALIBRATION } from '../subworkflows/nf-core/prepare_recalibration' addParams(
     baserecalibrator_options:        modules['baserecalibrator'],
     gatherbqsrreports_options:       modules['gatherbqsrreports']
 )
-include { RECALIBRATE } from '../subworkflow/local/recalibrate' addParams(
+include { PREPARE_RECALIBRATION_CSV } from '../subworkflows/local/prepare_recalibration_csv'
+include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' addParams(
     applybqsr_options:               modules['applybqsr'],
     merge_bam_options:               modules['merge_bam_recalibrate'],
     qualimap_bamqc_options:          modules['qualimap_bamqc_recalibrate'],
     samtools_index_options:          modules['samtools_index_recalibrate'],
     samtools_stats_options:          modules['samtools_stats_recalibrate']
 )
-include { GERMLINE_VARIANT_CALLING } from '../subworkflow/local/germline_variant_calling' addParams(
+include { RECALIBRATE_CSV } from '../subworkflows/local/recalibrate_csv'
+include { GERMLINE_VARIANT_CALLING } from '../subworkflows/local/germline_variant_calling' addParams(
     concat_gvcf_options:             modules['concat_gvcf'],
     concat_haplotypecaller_options:  modules['concat_haplotypecaller'],
     genotypegvcf_options:            modules['genotypegvcf'],
     haplotypecaller_options:         modules['haplotypecaller'],
     strelka_options:                 modules['strelka_germline']
 )
-// include { TUMOR_VARIANT_CALLING } from '../subworkflow/local/tumor_variant_calling' addParams(
+// include { TUMOR_VARIANT_CALLING } from '../subworkflows/local/tumor_variant_calling' addParams(
 // )
-include { PAIR_VARIANT_CALLING } from '../subworkflow/local/pair_variant_calling' addParams(
+include { PAIR_VARIANT_CALLING } from '../subworkflows/local/pair_variant_calling' addParams(
     manta_options:                   modules['manta_somatic'],
-    msisensor_msi_options:           modules['msisensor_msi'],
+    msisensorpro_msi_options:        modules['msisensorpro_msi'],
     strelka_bp_options:              modules['strelka_somatic_bp'],
     strelka_options:                 modules['strelka_somatic']
 )
@@ -233,7 +193,7 @@ include { MULTIQC }                       from '../modules/nf-core/software/mult
 /* --       INCLUDE NF-CORE SUBWORKFLOWS       -- */
 ////////////////////////////////////////////////////
 
-include { FASTQC_TRIMGALORE }             from '../subworkflow/nf-core/fastqc_trimgalore' addParams(
+include { FASTQC_TRIMGALORE }             from '../subworkflows/nf-core/fastqc_trimgalore' addParams(
     fastqc_options:                  modules['fastqc'],
     trimgalore_options:              modules['trimgalore']
 )
@@ -247,12 +207,11 @@ workflow SAREK {
     BUILD_INDICES(
         dbsnp,
         fasta,
+        fasta_fai,
         germline_resource,
         known_indels,
         pon,
-        step,
-        target_bed,
-        tools)
+        target_bed)
 
     intervals = BUILD_INDICES.out.intervals
 
@@ -265,7 +224,10 @@ workflow SAREK {
     known_indels_tbi      = params.known_indels      ? params.known_indels_index      ? file(params.known_indels_index)      : BUILD_INDICES.out.known_indels_tbi.collect() : []
     pon_tbi               = params.pon               ? params.pon_index               ? file(params.pon_index)               : BUILD_INDICES.out.pon_tbi                    : []
 
-    msisensor_scan    = BUILD_INDICES.out.msisensor_scan
+    known_sites     = [dbsnp, known_indels]
+    known_sites_tbi = dbsnp_tbi.mix(known_indels_tbi).collect()
+
+    msisensorpro_scan = BUILD_INDICES.out.msisensorpro_scan
     target_bed_gz_tbi = BUILD_INDICES.out.target_bed_gz_tbi
 
     ////////////////////////////////////////////////////
@@ -282,140 +244,186 @@ workflow SAREK {
     // trim only with `--trim_fastq`
     // additional options to be set up
 
-    FASTQC_TRIMGALORE(
-        input_sample,
-        ('fastqc' in skip_qc || step != "mapping"),
-        !(params.trim_fastq))
-
-    reads_input = FASTQC_TRIMGALORE.out.reads
-
-    qc_reports = qc_reports.mix(
-        FASTQC_TRIMGALORE.out.fastqc_html,
-        FASTQC_TRIMGALORE.out.fastqc_zip,
-        FASTQC_TRIMGALORE.out.trim_html,
-        FASTQC_TRIMGALORE.out.trim_log,
-        FASTQC_TRIMGALORE.out.trim_zip)
-
-    // STEP 1: MAPPING READS TO REFERENCE GENOME WITH BWA-MEM
-
-    MAPPING(
-        ('bamqc' in skip_qc),
-        ('samtools' in skip_qc),
-        bwa,
-        fai,
-        fasta,
-        reads_input,
-        save_bam_mapped,
-        step,
-        target_bed)
-
-    bam_mapped    = MAPPING.out.bam
-    bam_mapped_qc = MAPPING.out.qc
-
-    qc_reports = qc_reports.mix(bam_mapped_qc)
-
-    // STEP 2: MARKING DUPLICATES
-
-    bam_markduplicates = channel.empty()
-
-    if (step == 'preparerecalibration') {
-        if (params.skip_markduplicates) bam_markduplicates = bam_mapped
-        else {
-            MARKDUPLICATES(bam_mapped, step)
+    if (params.step == 'mapping') {
+        FASTQC_TRIMGALORE(
+            input_sample,
+            !(params.trim_fastq))
+
+        reads_input = FASTQC_TRIMGALORE.out.reads
+
+        qc_reports = qc_reports.mix(
+            FASTQC_TRIMGALORE.out.fastqc_html,
+            FASTQC_TRIMGALORE.out.fastqc_zip,
+            FASTQC_TRIMGALORE.out.trim_html,
+            FASTQC_TRIMGALORE.out.trim_log,
+            FASTQC_TRIMGALORE.out.trim_zip)
+
+        // STEP 1: MAPPING READS TO REFERENCE GENOME
+        MAPPING(
+            'bamqc' in params.skip_qc,
+            'samtools' in params.skip_qc,
+            params.aligner,
+            bwa,
+            fai,
+            fasta,
+            reads_input,
+            target_bed)
+
+        bam_mapped    = MAPPING.out.bam
+        bam_mapped_qc = MAPPING.out.qc
+
+        qc_reports = qc_reports.mix(bam_mapped_qc)
+
+        // Create CSV to restart from this step
+        MAPPING_CSV(bam_mapped, save_bam_mapped, params.skip_markduplicates)
+
+        if (params.skip_markduplicates) {
+            bam_markduplicates = bam_mapped
+        } else {
+            // STEP 2: MARKING DUPLICATES
+            MARKDUPLICATES(bam_mapped, params.use_gatk_spark, !('markduplicates' in params.skip_qc))
             bam_markduplicates = MARKDUPLICATES.out.bam
+
+            // Create CSV to restart from this step
+            MARKDUPLICATES_CSV(bam_markduplicates)
         }
     }
 
-    if (step == 'preparerecalibration') bam_markduplicates = input_sample
-
-    // STEP 3: CREATING RECALIBRATION TABLES
+    if (params.step.toLowerCase() == 'prepare_recalibration') bam_markduplicates = input_sample
 
-    PREPARE_RECALIBRATION(
-        bam_markduplicates,
-        dbsnp,
-        dbsnp_tbi,
-        dict,
-        fai,
-        fasta,
-        intervals,
-        known_indels,
-        known_indels_tbi,
-        step)
-
-    table_bqsr = PREPARE_RECALIBRATION.out.table_bqsr
-
-    // STEP 4: RECALIBRATING
-    bam_applybqsr = bam_markduplicates.join(table_bqsr)
-
-    if (step == 'recalibrate') bam_applybqsr = input_sample
-
-    RECALIBRATE(
-        ('bamqc' in skip_qc),
-        ('samtools' in skip_qc),
-        bam_applybqsr,
-        dict,
-        fai,
-        fasta,
-        intervals,
-        step,
-        target_bed)
+    if (params.step.toLowerCase() in ['mapping', 'prepare_recalibration']) {
+        // STEP 3: CREATING RECALIBRATION TABLES
+        PREPARE_RECALIBRATION(
+            bam_markduplicates,
+            dict,
+            fai,
+            fasta,
+            intervals,
+            known_sites,
+            known_sites_tbi,
+            params.no_intervals)
 
-    bam_recalibrated    = RECALIBRATE.out.bam
-    bam_recalibrated_qc = RECALIBRATE.out.qc
+        table_bqsr = PREPARE_RECALIBRATION.out.table_bqsr
+        PREPARE_RECALIBRATION_CSV(table_bqsr)
 
-    qc_reports = qc_reports.mix(bam_recalibrated_qc)
+        bam_applybqsr = bam_markduplicates.join(table_bqsr)
+    }
 
-    bam_variant_calling = bam_recalibrated
+    if (params.step.toLowerCase() == 'recalibrate') bam_applybqsr = input_sample
 
-    if (step == 'variantcalling') bam_variant_calling = input_sample
+    if (params.step.toLowerCase() in ['mapping', 'prepare_recalibration', 'recalibrate']) {
+        // STEP 4: RECALIBRATING
+        RECALIBRATE(
+            ('bamqc' in params.skip_qc),
+            ('samtools' in params.skip_qc),
+            bam_applybqsr,
+            dict,
+            fai,
+            fasta,
+            intervals,
+            target_bed)
 
-    ////////////////////////////////////////////////////
-    /* --         GERMLINE VARIANT CALLING         -- */
-    ////////////////////////////////////////////////////
+        bam_recalibrated    = RECALIBRATE.out.bam
+        bam_recalibrated_qc = RECALIBRATE.out.qc
 
-    GERMLINE_VARIANT_CALLING(
-        bam_variant_calling,
-        dbsnp,
-        dbsnp_tbi,
-        dict,
-        fai,
-        fasta,
-        intervals,
-        target_bed,
-        target_bed_gz_tbi,
-        tools)
+        RECALIBRATE_CSV(bam_recalibrated)
 
-    ////////////////////////////////////////////////////
-    /* --          SOMATIC VARIANT CALLING         -- */
-    ////////////////////////////////////////////////////
+        qc_reports = qc_reports.mix(bam_recalibrated_qc)
 
-    // TUMOR_VARIANT_CALLING(
-    //     bam_variant_calling,
-    //     dbsnp,
-    //     dbsnp_tbi,
-    //     dict,
-    //     fai,
-    //     fasta,
-    //     intervals,
-    //     target_bed,
-    //     target_bed_gz_tbi,
-    //     tools)
-
-    PAIR_VARIANT_CALLING(
-        bam_variant_calling,
-        dbsnp,
-        dbsnp_tbi,
-        dict,
-        fai,
-        fasta,
-        intervals,
-        msisensor_scan,
-        target_bed,
-        target_bed_gz_tbi,
-        tools)
+        bam_variant_calling = bam_recalibrated
+    }
 
-    ////////////////////////////////////////////////////
-    /* --                ANNOTATION                -- */
-    ////////////////////////////////////////////////////
+    if (params.step.toLowerCase() == 'variant_calling') bam_variant_calling = input_sample
+
+    if (params.tools != null) {
+
+        ////////////////////////////////////////////////////
+        /* --         GERMLINE VARIANT CALLING         -- */
+        ////////////////////////////////////////////////////
+    
+        GERMLINE_VARIANT_CALLING(
+            bam_variant_calling,
+            dbsnp,
+            dbsnp_tbi,
+            dict,
+            fai,
+            fasta,
+            intervals,
+            target_bed,
+            target_bed_gz_tbi)
+
+        ////////////////////////////////////////////////////
+        /* --          SOMATIC VARIANT CALLING         -- */
+        ////////////////////////////////////////////////////
+
+        // TUMOR_VARIANT_CALLING(
+        //     bam_variant_calling,
+        //     dbsnp,
+        //     dbsnp_tbi,
+        //     dict,
+        //     fai,
+        //     fasta,
+        //     intervals,
+        //     target_bed,
+        //     target_bed_gz_tbi)
+
+        PAIR_VARIANT_CALLING(
+            bam_variant_calling,
+            dbsnp,
+            dbsnp_tbi,
+            dict,
+            fai,
+            fasta,
+            intervals,
+            msisensorpro_scan,
+            target_bed,
+            target_bed_gz_tbi)
+
+        ////////////////////////////////////////////////////
+        /* --                ANNOTATION                -- */
+        ////////////////////////////////////////////////////
+    }
+}
 
+def extract_csv(csv_file) {
+    Channel.from(csv_file).splitCsv(header: true).map{ row ->
+        def meta = [:]
+
+        meta.patient = row.patient.toString()
+        meta.sample  = row.sample.toString()
+
+        // If no gender specified, gender is not considered (only used for somatic CNV)
+        if (row.gender == null) {
+            meta.gender = "NA"
+        } else meta.gender = row.gender.toString()
+
+        // If no status specified, sample is considered normal
+        if (row.status == null) {
+            meta.status = 0
+        } else meta.status = row.status.toInteger()
+
+        if (row.lane != null) {
+        // mapping with fastq
+            meta.id         = "${row.sample}-${row.lane}".toString()
+            def read1       = file(row.fastq1, checkIfExists: true)
+            def read2       = file(row.fastq2, checkIfExists: true)
+            def CN          = params.sequencing_center ? "CN:${params.sequencing_center}\\t" : ''
+            def read_group  = "\"@RG\\tID:${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.sample}\\tLB:${row.sample}\\tPL:ILLUMINA\""
+            meta.read_group = read_group.toString()
+            return [meta, [read1, read2]]
+        } else if (row.table != null) {
+        // recalibration
+            meta.id = meta.sample
+            def bam     = file(row.bam, checkIfExists: true)
+            def bai     = file(row.bai, checkIfExists: true)
+            def table   = file(row.table, checkIfExists: true)
+            return [meta, bam, bai, table]
+        } else {
+        // prepare_recalibration or variant_calling
+            meta.id = meta.sample
+            def bam     = file(row.bam, checkIfExists: true)
+            def bai     = file(row.bai, checkIfExists: true)
+            return [meta, bam, bai]
+        }
+    }
 }
\ No newline at end of file