Merge pull request #485 from maxulysse/dev_skip

modules config update - preprocessing refactor
nf-core · Feb 20, 2022 · 66d66e0 · 66d66e0
2 parents f1bcc42 + 096f97d
commit 66d66e0
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Showing 112 changed files with 1,995 additions and 1,959 deletions.
diff --git a/conf/modules.config b/conf/modules.config
diff --git a/conf/test.config b/conf/test.config
@@ -50,6 +50,9 @@ profiles {
         params.input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/tiny-vcf-https.csv'
         params.step                = 'annotate'
     }
+    no_intervals {
+        params.no_intervals        = true
+    }
     pair {
         params.input               = "${baseDir}/tests/csv/3.0/fastq_pair.csv"
     }
@@ -61,15 +64,12 @@ profiles {
         params.save_bam_mapped     = true
     }
     skip_markduplicates {
-        params.skip_markduplicates = true
+        params.skip_tools          = "markduplicates"
     }
     split_fastq {
         params.split_fastq         = 150000
         params.save_split_fastqs   = true
     }
-    no_intervals {
-        params.no_intervals          = true
-    }
     targeted {
         params.intervals           = "${params.genomes_base}/data/genomics/homo_sapiens/genome/multi_intervals.bed"
         params.wes                 = true
@@ -96,21 +96,21 @@ profiles {
         params.three_prime_clip_r2 = 1
         params.trim_fastq          = true
     }
-    use_gatk_spark {
-        params.use_gatk_spark      = 'bqsr,markduplicates'
-    }
     umi {
         params.input               = "${baseDir}/tests/csv/3.0/fastq_umi.csv"
         params.umi_read_structure  = '7M1S+T'
     }
+    use_gatk_spark {
+        params.use_gatk_spark      = 'baserecalibrator,markduplicates'
+    }
 }
 
 //This is apparently useless as it won't overwrite things in the modules.config
 process {
-    withName:SNPEFF {
+    withName:ENSEMBLVEP {
         maxForks = 1
     }
-    withName:ENSEMBLVEP {
+    withName:SNPEFF {
         maxForks = 1
     }
 }
diff --git a/modules.json b/modules.json
@@ -4,106 +4,106 @@
     "repos": {
         "nf-core/modules": {
             "bcftools/stats": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwa/index": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwa/mem": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwamem2/index": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwamem2/mem": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "cat/fastq": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "cnvkit/batch": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "deepvariant": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "ensemblvep": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "fastqc": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "fgbio/callmolecularconsensusreads": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "fgbio/fastqtobam": {
-                "git_sha": "e3285528aca2733ff2d544cb5e5fcc34599226f3"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "fgbio/groupreadsbyumi": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "freebayes": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/applybqsr": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/applyvqsr": {
-                "git_sha": "598d7abdb2a8df1aa3471c48d9186a9e3465983f"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/baserecalibrator": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/calculatecontamination": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/createsequencedictionary": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/estimatelibrarycomplexity": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/filtermutectcalls": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/gatherbqsrreports": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/genomicsdbimport": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "967fb22dedc2c8855f00e64c3d7b5814c85242a6"
             },
             "gatk4/genotypegvcfs": {
-                "git_sha": "598d7abdb2a8df1aa3471c48d9186a9e3465983f"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/getpileupsummaries": {
-                "git_sha": "f5d5926516d2319c1af83fb4b33834cc4461ce62"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/haplotypecaller": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/learnreadorientationmodel": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/markduplicates": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/mutect2": {
-                "git_sha": "f5d5926516d2319c1af83fb4b33834cc4461ce62"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/variantrecalibrator": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "manta/germline": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "manta/somatic": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "manta/tumoronly": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "msisensorpro/msi_somatic": {
                 "git_sha": "c8ebd0de36c649a14fc92f2f73cbd9f691a8ce0a"
@@ -112,58 +112,58 @@
                 "git_sha": "c8ebd0de36c649a14fc92f2f73cbd9f691a8ce0a"
             },
             "multiqc": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samblaster": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/bam2fq": {
-                "git_sha": "e751e5040af57e1b4e06ed4e0f3efe6de25c1683"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/faidx": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/index": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/merge": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/mpileup": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/stats": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/view": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "seqkit/split2": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "snpeff": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "strelka/germline": {
-                "git_sha": "f5d5926516d2319c1af83fb4b33834cc4461ce62"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "strelka/somatic": {
-                "git_sha": "f5d5926516d2319c1af83fb4b33834cc4461ce62"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "tabix/bgziptabix": {
-                "git_sha": "e22966ce74340cb671576143e5fdbbd71670cffa"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "tabix/tabix": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "tiddit/sv": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "trimgalore": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "vcftools": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             }
         }
     }

diff --git a/modules/local/bgzip.nf b/modules/local/bgzip.nf
@@ -15,6 +15,9 @@ process BGZIP {
     tuple val(meta), path("*.vcf"), emit: vcf
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/build_intervals/main.nf b/modules/local/build_intervals/main.nf
@@ -13,6 +13,9 @@ process BUILD_INTERVALS {
     output:
     path "*.bed", emit: bed
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     awk -v FS='\t' -v OFS='\t' '{ print \$1, \"0\", \$2 }' ${fasta_fai} > ${fasta_fai.baseName}.bed

diff --git a/modules/local/concat_vcf/main.nf b/modules/local/concat_vcf/main.nf
@@ -17,13 +17,16 @@ process CONCAT_VCF {
     tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi
     path  "versions.yml"                         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args  ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def target_options   = target_bed ? "-t ${target_bed}" : ""
-
     """
     concatenateVCFs.sh -i ${fasta_fai} -c ${task.cpus} -o ${prefix}.vcf ${target_options} $args
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')

diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf
@@ -14,6 +14,9 @@ process CREATE_INTERVALS_BED {
     path ("*.bed"), emit: bed
     //TODO version number missing
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     // If intervals file is in BED format,
     // Fifth column is interpreted to contain runtime estimates

diff --git a/modules/local/deeptools/bamcoverage.nf b/modules/local/deeptools/bamcoverage.nf
@@ -14,10 +14,12 @@ process DEEPTOOLS_BAMCOVERAGE {
     tuple val(meta), path("*.bigWig"), emit: bigwig
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     bamCoverage \
     --bam $bam \

diff --git a/modules/local/gatk4/applybqsrspark/main.nf b/modules/local/gatk4/applybqsrspark/main.nf
@@ -16,6 +16,9 @@ process GATK4_APPLYBQSR_SPARK {
     tuple val(meta), path("*.cram"), emit: cram
     path "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args  ?: ''
     def avail_mem = 3

diff --git a/modules/local/gatk4/baserecalibratorspark/main.nf b/modules/local/gatk4/baserecalibratorspark/main.nf
@@ -18,6 +18,9 @@ process GATK4_BASERECALIBRATOR_SPARK {
     tuple val(meta), path("*.table"), emit: table
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args  ?: ''
     def avail_mem = 3

diff --git a/modules/local/gatk4/gatherpileupsummaries.nf b/modules/local/gatk4/gatherpileupsummaries.nf
@@ -17,6 +17,9 @@ process GATK4_GATHERPILEUPSUMMARIES {
     tuple val(meta), path("*.table"), emit: table
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

diff --git a/modules/local/gatk4/intervallisttobed.nf b/modules/local/gatk4/intervallisttobed.nf
@@ -14,6 +14,9 @@ process GATK4_INTERVALLISTTOBED {
     tuple val(meta), path("*.bed"), emit: bed
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,6 +13,9 @@ process BUILD_INTERVALS { @@
         output:
         path "*.bed", emit: bed
+        when:
+        task.ext.when == null || task.ext.when
         script:
         """
         awk -v FS='\t' -v OFS='\t' '{ print \$1, \"0\", \$2 }' ${fasta_fai} > ${fasta_fai.baseName}.bed
@@ Expand Down @@