Cnv for real now

.github/workflows/ci.yml

@@ -34,6 +34,7 @@ jobs:
           - "aligner"
           - "annotation"
           - "default"
+          - "controlfreec"
           - "deepvariant"
           - "freebayes"
           - "gatk4_spark"

conf/igenomes.config

@@ -16,7 +16,6 @@ params {
             ac_loci_gc            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
             bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/"
             chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
-            chr_length            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len"
             dbsnp                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf"
             dbsnp_tbi             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
             dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
@@ -40,7 +39,6 @@ params {
             bwamem2               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
             hashmap               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
             chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
-            chr_length            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
             dbsnp                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
             dbsnp_tbi             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
             dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
@@ -69,7 +67,6 @@ params {
         'GRCm38' {
             bwa                   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
             chr_dir               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
-            chr_length            = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len"
             dbsnp                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
             dbsnp_tbi             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
             dict                  = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"

conf/modules.config

@@ -227,7 +227,7 @@ process {
 
 // SPLIT FASTQ
 
-    withName: "SEQKIT_SPLIT2" {
+    withName: 'SEQKIT_SPLIT2' {
         ext.args         = { "--by-size ${params.split_fastq}" }
         ext.when         = { params.split_fastq > 1 }
         publishDir       = [
@@ -521,7 +521,7 @@ process{
     withName: 'CONCAT_HAPLOTYPECALLER' {
         ext.prefix       = {"${meta.id}.g"}
         publishDir       = [
-            enabled: "${params.generate_gvcf}",
+            enabled: "${!params.no_intervals }",
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" }
         ]
@@ -531,7 +531,7 @@ process{
         ext.prefix       = {"${meta.id}.g"}
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') }
         publishDir       = [
-            enabled: "${params.no_intervals || params.generate_gvcf}",
+            enabled: "${params.no_intervals}",
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller"},
             pattern: "*{vcf.gz,vcf.gz.tbi}"
@@ -540,19 +540,12 @@ process{
     withName: 'GENOTYPEGVCFS' {
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline}
         publishDir       = [
-            enabled: true,
+            enabled: "${params.generate_gvcf}",
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller"},
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
-    withName : 'TABIX_VC_HAPLOTYPECALLER' {
-        publishDir       = [
-            enabled: "${params.generate_gvcf}",
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" }
-        ]
-    }
 
     // MANTA
     withName: 'CONCAT_MANTA.*' {
@@ -619,6 +612,103 @@ process{
 
 // TUMOR_VARIANT_CALLING
 
+    //CONTROLFREEC
+    withName: 'ASSESS_SIGNIFICANCE' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{.p.value.txt}"
+        ]
+    }
+
+    withName: 'CAT_MPILEUP_.*' {
+        ext.when =  { !params.no_intervals }
+        publishDir       = [
+            enabled: "${!params.no_intervals}",
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{mpileup}"
+        ]
+    }
+
+    withName: 'FREEC_.*' {
+        ext.when         = { params.tools && params.tools.contains('controlfreec') }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{BedGraph,cpn,txt,_CNVs}"
+        ]
+    }
+
+    withName: 'FREEC_TUMORONLY'{
+        ext.args = {[
+                    "sample":[
+                        inputformat: 'pileup',
+                        mateorientation: 'FR'
+                    ],
+                    "general" :[
+                        bedgraphoutput: "TRUE",
+                        breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs
+                        breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs
+                        coefficientofvariation: params.cf_coeff,
+                        contamination: params.cf_contamination ?: "",
+                        contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "",
+                        forcegccontentnormalization: params.wes ? "1" : "0",
+                        minimalsubclonepresence: params.wes ? "30" : "20",
+                        noisydata: params.wes ? "TRUE" : "FALSE",
+                        ploidy: params.ploidy,
+                        printNA:  params.wes ? "FALSE" : "TRUE",
+                        readcountthreshold:  params.wes ? "50" : "10",
+                        sex: meta.gender,
+                        //uniquematch: not set
+                        window: params.cf_window ?: ""
+                        ],
+                    "BAF":[
+                        minimalcoverageperposition: params.cf_mincov ?: "",
+                        minimalqualityperposition: params.cf_minqual ?: "",
+                        //"shiftinquality": (optional)not set
+                    ]
+                ]
+            }
+    }
+
+    withName: 'FREEC2BED' {
+        ext.args = { "${params.ploidy}" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{.bed}"
+        ]
+    }
+
+    withName: 'FREEC2CIRCOS' {
+        ext.args = { "${params.ploidy}" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{.circos.txt}"
+        ]
+    }
+
+    withName: 'MAKEGRAPH' {
+        ext.args = { "${params.ploidy}" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{png}"
+        ]
+    }
+
+    withName: 'MPILEUP_.*' {
+        ext.when         = { params.tools && params.tools.contains('controlfreec') }
+        publishDir       = [
+            enabled: "${params.no_intervals}",
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            pattern: "*{mpileup}"
+        ]
+    }
+
     //MANTA
     withName: 'CONCAT_MANTA_TUMOR' {
         ext.prefix       = {"${meta.id}.tumor_sv"}
@@ -691,13 +781,86 @@ process{
 
 // PAIR_VARIANT_CALLING
 
+    //ASCAT
+    withName: 'ASCAT' {
+        ext.args = {
+            [
+            "gender": meta.sex,
+            //"genomeVersion": "hg19"
+            //"purity": (optional),
+            //"ploidy": params.ploidy,
+            //"gc_files": (optional),
+            //"minCounts": (optional),
+            //"chrom_names": (optional),
+            //"min_base_qual": (optional),
+            //"min_map_qual": (optional),
+            //"ref_fasta": (optional),
+            //"skip_allele_counting_tumour": (optional),
+            //"skip_allele_counting_normal": (optional)
+            ]
+        }
+    }
+
+    //CONTROLFREEC
+    withName: 'MPILEUP_NORMAL' {
+        ext.prefix = { "${meta.id}.normal" }
+    }
+
+    withName: 'MPILEUP_TUMOR' {
+        ext.prefix = { "${meta.id}.tumor" }
+    }
+
+    withName: 'CAT_MPILEUP_NORMAL' {
+        ext.prefix = { "${meta.id}.normal.mpileup" }
+    }
+
+    withName: 'CAT_MPILEUP_TUMOR' {
+        ext.prefix = { "${meta.id}.tumor.mpileup" }
+    }
+
+    withName: 'FREEC_SOMATIC'{
+        ext.args = {[
+                    "sample":[
+                        inputformat: 'pileup',
+                        mateorientation: 'FR'
+                    ],
+                    "control":[
+                        inputformat: "pileup",
+                        mateorientation: "FR"
+                    ],
+                    "general" :[
+                        bedgraphoutput: "TRUE",
+                        breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs
+                        breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs
+                        coefficientofvariation: params.cf_coeff,
+                        contamination: params.cf_contamination ?: "",
+                        contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "",
+                        forcegccontentnormalization: params.wes ? "1" : "0",
+                        minimalsubclonepresence: params.wes ? "30" : "20",
+                        noisydata: params.wes ? "TRUE" : "FALSE",
+                        ploidy: params.ploidy,
+                        printNA:  params.wes ? "FALSE" : "TRUE",
+                        readcountthreshold:  params.wes ? "50" : "10",
+                        sex: meta.gender,
+                        //uniquematch: not set
+                        window: params.cf_window ?: ""
+                        ],
+                    "BAF":[
+                        minimalcoverageperposition: params.cf_mincov ?: "",
+                        minimalqualityperposition: params.cf_minqual ?: "",
+                        //"shiftinquality": (optional)not set
+                    ]
+                ]
+            }
+    }
+
     //MANTA
     withName: 'CONCAT_MANTA_SOMATIC' {
         ext.prefix       = {"${meta.id}.somatic_sv"}
     }
 
     //MUTECT2
-    withName: 'CALCULATECONTAMINATION'{
+    withName: 'CALCULATECONTAMINATION' {
         //ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -716,7 +879,7 @@ process{
         ]
     }
 
-    withName: 'LEARNREADORIENTATIONMODEL'{
+    withName: 'LEARNREADORIENTATIONMODEL' {
         ext.prefix         = { "${meta.id}.learnreadorientationmodel" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -725,7 +888,7 @@ process{
     }
 
     //MSISENSORPRO
-    withName: 'MSISENSORPRO_MSI_SOMATIC'{
+    withName: 'MSISENSORPRO_MSI_SOMATIC' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/msisensorpro" },

conf/test.config

@@ -123,6 +123,7 @@ profiles {
         params.wes                 = true
         params.genome              = 'WBcel235'
         params.vep_genome          = 'WBcel235'
+        params.chr_dir             = "${params.genomes_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
     }
     trimming {
         params.clip_r1             = 1

main.nf

@@ -32,7 +32,6 @@ params.ac_loci_gc            = WorkflowMain.getGenomeAttribute(params, 'ac_loci_
 params.bwa                   = WorkflowMain.getGenomeAttribute(params, 'bwa')
 params.bwamem2               = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
 params.chr_dir               = WorkflowMain.getGenomeAttribute(params, 'chr_dir')
-params.chr_length            = WorkflowMain.getGenomeAttribute(params, 'chr_length')
 params.dbsnp                 = WorkflowMain.getGenomeAttribute(params, 'dbsnp')
 params.dbsnp_tbi             = WorkflowMain.getGenomeAttribute(params, 'dbsnp_tbi')
 params.dict                  = WorkflowMain.getGenomeAttribute(params, 'dict')