GATK4 first round without MuTect1 and indel realignment

annotate.nf

@@ -73,23 +73,23 @@ vcfToAnnotate = Channel.create()
 vcfNotToAnnotate = Channel.create()
 
 if (annotateVCF == []) {
+// we annote all available vcfs by default that we can find in the VariantCalling directory
   Channel.empty().mix(
     Channel.fromPath("${directoryMap.haplotypecaller}/*.vcf.gz")
       .flatten().map{vcf -> ['haplotypecaller', vcf]},
     Channel.fromPath("${directoryMap.manta}/*SV.vcf.gz")
       .flatten().map{vcf -> ['manta', vcf]},
-    Channel.fromPath("${directoryMap.mutect1}/*.vcf.gz")
-      .flatten().map{vcf -> ['mutect1', vcf]},
     Channel.fromPath("${directoryMap.mutect2}/*.vcf.gz")
       .flatten().map{vcf -> ['mutect2', vcf]},
-    Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz")
+    Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz")		// Strelka only
       .flatten().map{vcf -> ['strelka', vcf]},
-    Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz")
+    Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz")	// Strelka with Manta indel candidates
       .flatten().map{vcf -> ['strelkabp', vcf]}
   ).choice(vcfToAnnotate, vcfNotToAnnotate) {
     annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1
   }
 } else if (annotateTools == []) {
+// alternatively, annotate user-submitted VCFs
   list = ""
   annotateVCF.each{ list += ",${it}" }
   list = list.substring(1)
@@ -101,6 +101,10 @@ if (annotateVCF == []) {
 
 vcfNotToAnnotate.close()
 
+// as now have the list of VCFs to annotate, the first step is to annotate with allele frequencies, if there are any
+
+
+
 (vcfForBCFtools, vcfForVCFtools, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(4)
 
 vcfForVep = vcfForVep.map {
@@ -224,11 +228,12 @@ process RunVEP {
   finalannotator = annotator == "snpeff" ? 'merge' : 'vep'
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
   """
-  vep \
+  vep --dir /opt/vep/.vep/ \
   -i ${vcf} \
   -o ${vcf.simpleName}_VEP.ann.vcf \
   --assembly ${genome} \
   --cache \
+	--cache_version 91 \
   --database \
   --everything \
   --filter_common \
@@ -346,7 +351,6 @@ def helpMessage() {
   log.info "       Possible values are:"
   log.info "         haplotypecaller (Annotate HaplotypeCaller output)"
   log.info "         manta (Annotate Manta output)"
-  log.info "         mutect1 (Annotate MuTect1 output)"
   log.info "         mutect2 (Annotate MuTect2 output)"
   log.info "         strelka (Annotate Strelka output)"
   log.info "    --annotateVCF"

buildContainers.nf

@@ -177,13 +177,6 @@ def grabRevision() {
 def defineContainersList(){
   // Return list of authorized containers
   return [
-    'freebayes',
-    'gatk',
-    'gatk4',
-    'igvtools',
-    'mutect1',
-    'picard',
-    'qctools',
     'r-base',
     'runallelecount',
     'sarek',
@@ -208,8 +201,7 @@ def helpMessage() {
   log.info "    --containers: Choose which containers to build"
   log.info "       Default: all"
   log.info "       Possible values:"
-  log.info "         all, freebayes, gatk, gatk4, igvtools, mutect1, picard"
-  log.info "         qctools, r-base, runallelecount, sarek, snpeff"
+  log.info "         all, r-base, runallelecount, sarek, snpeff"
   log.info "         snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
   log.info "    --docker: Build containers using Docker"
   log.info "    --help"

buildReferences.nf

@@ -29,7 +29,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - ProcessReference - Download all references if needed
  - DecompressFile - Extract files if needed
  - BuildBWAindexes - Build indexes for BWA
- - BuildPicardIndex - Build index with Picard
+ - BuildReferenceIndex - Build index for FASTA refs
  - BuildSAMToolsIndex - Build index with SAMTools
  - BuildVCFIndex - Build index for VCF files
 ================================================================================
@@ -98,7 +98,7 @@ if (params.verbose) ch_decompressedFiles = ch_decompressedFiles.view {
 
 ch_fastaFile = Channel.create()
 ch_fastaForBWA = Channel.create()
-ch_fastaForPicard = Channel.create()
+ch_fastaReference = Channel.create()
 ch_fastaForSAMTools = Channel.create()
 ch_otherFile = Channel.create()
 ch_vcfFile = Channel.create()
@@ -108,7 +108,7 @@ ch_decompressedFiles
     it =~ ".fasta" ? 0 :
     it =~ ".vcf" ? 1 : 2}
 
-(ch_fastaForBWA, ch_fastaForPicard, ch_fastaForSAMTools, ch_fastaFileToKeep) = ch_fastaFile.into(4)
+(ch_fastaForBWA, ch_fastaReference, ch_fastaForSAMTools, ch_fastaFileToKeep) = ch_fastaFile.into(4)
 (ch_vcfFile, ch_vcfFileToKeep) = ch_vcfFile.into(2)
 
 ch_notCompressedfiles
@@ -137,29 +137,28 @@ if (params.verbose) bwaIndexes.flatten().view {
   "BWA index           : ${it.fileName}"
 }
 
-process BuildPicardIndex {
+process BuildReferenceIndex {
   tag {f_reference}
 
   publishDir params.outDir, mode: 'link'
 
   input:
-    file(f_reference) from ch_fastaForPicard
+    file(f_reference) from ch_fastaReference
 
   output:
-    file("*.dict") into ch_picardIndex
+    file("*.dict") into ch_referenceIndex
 
   script:
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$PICARD_HOME/picard.jar \
+  gatk --java-options "-Xmx${task.memory.toGiga()}g" \
   CreateSequenceDictionary \
-  REFERENCE=${f_reference} \
-  OUTPUT=${f_reference.baseName}.dict
+  --REFERENCE ${f_reference} \
+  --OUTPUT ${f_reference.baseName}.dict
   """
 }
 
-if (params.verbose) ch_picardIndex.view {
-  "Picard index        : ${it.fileName}"
+if (params.verbose) ch_referenceIndex.view {
+  "Reference index        : ${it.fileName}"
 }
 
 process BuildSAMToolsIndex {
@@ -196,7 +195,7 @@ process BuildVCFIndex {
 
   script:
   """
-  \$IGVTOOLS_HOME/igvtools index ${f_reference}
+  igvtools index ${f_reference}
   """
 }
 

configuration/containers.config

@@ -9,52 +9,48 @@
 
 process {
   $BuildBWAindexes.container          = "${params.repository}/sarek:${params.tag}"
-  $BuildPicardIndex.container         = "${params.repository}/picard:${params.tag}"
+  $BuildReferenceIndex.container         = "${params.repository}/sarek:${params.tag}"
   $BuildSAMToolsIndex.container       = "${params.repository}/sarek:${params.tag}"
-  $BuildVCFIndex.container            = "${params.repository}/igvtools:${params.tag}"
+  $BuildVCFIndex.container            = "${params.repository}/sarek:${params.tag}"
   $CompressVCF.container              = "${params.repository}/sarek:${params.tag}"
   $ConcatVCF.container                = "${params.repository}/sarek:${params.tag}"
-  $CreateRecalibrationTable.container = "${params.repository}/gatk:${params.tag}"
-  $GetVersionAll.container            = "${params.repository}/qctools:${params.tag}"
+  $CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
+  $GetVersionAll.container            = "${params.repository}/sarek:${params.tag}"
   $GetVersionAlleleCount.container    = "${params.repository}/runallelecount:${params.tag}"
   $GetVersionASCAT.container          = "${params.repository}/r-base:${params.tag}"
-  $GetVersionBamQC.container          = "${params.repository}/qctools:${params.tag}"
+  $GetVersionBamQC.container          = "${params.repository}/sarek:${params.tag}"
   $GetVersionBCFtools.container       = "${params.repository}/sarek:${params.tag}"
   $GetVersionBWAsamtools.container    = "${params.repository}/sarek:${params.tag}"
-  $GetVersionFastQC.container         = "${params.repository}/qctools:${params.tag}"
-  $GetVersionFreeBayes.container      = "${params.repository}/freebayes:${params.tag}"
-  $GetVersionGATK.container           = "${params.repository}/gatk:${params.tag}"
+  $GetVersionFastQC.container         = "${params.repository}/sarek:${params.tag}"
+  $GetVersionFreeBayes.container      = "${params.repository}/sarek:${params.tag}"
+  $GetVersionGATK.container           = "${params.repository}/sarek:${params.tag}"
   $GetVersionManta.container          = "${params.repository}/sarek:${params.tag}"
-  $GetVersionPicard.container         = "${params.repository}/picard:${params.tag}"
   $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   $GetVersionStrelka.container        = "${params.repository}/sarek:${params.tag}"
-  $GetVersionVCFtools.container       = "${params.repository}/qctools:${params.tag}"
+  $GetVersionVCFtools.container       = "${params.repository}/sarek:${params.tag}"
   $GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
-  $IndelRealigner.container           = "${params.repository}/gatk:${params.tag}"
   $MapReads.container                 = "${params.repository}/sarek:${params.tag}"
-  $MarkDuplicates.container           = "${params.repository}/picard:${params.tag}"
+  $MarkDuplicates.container           = "${params.repository}/sarek:${params.tag}"
   $MergeBams.container                = "${params.repository}/sarek:${params.tag}"
-  $RealignerTargetCreator.container   = "${params.repository}/gatk:${params.tag}"
-  $RecalibrateBam.container           = "${params.repository}/gatk:${params.tag}"
+  $RecalibrateBam.container           = "${params.repository}/sarek:${params.tag}"
   $RunAlleleCount.container           = "${params.repository}/runallelecount:${params.tag}"
   $RunAscat.container                 = "${params.repository}/r-base:${params.tag}"
-  $RunBamQC.container                 = "${params.repository}/qctools:${params.tag}"
+  $RunBamQC.container                 = "${params.repository}/sarek:${params.tag}"
   $RunBcftoolsStats.container         = "${params.repository}/sarek:${params.tag}"
   $RunConvertAlleleCounts.container   = "${params.repository}/r-base:${params.tag}"
-  $RunFastQC.container                = "${params.repository}/qctools:${params.tag}"
-  $RunFreeBayes.container             = "${params.repository}/freebayes:${params.tag}"
-  $RunGenotypeGVCFs.container         = "${params.repository}/gatk:${params.tag}"
-  $RunHaplotypecaller.container       = "${params.repository}/gatk:${params.tag}"
+  $RunFastQC.container                = "${params.repository}/sarek:${params.tag}"
+  $RunFreeBayes.container             = "${params.repository}/sarek:${params.tag}"
+  $RunGenotypeGVCFs.container         = "${params.repository}/sarek:${params.tag}"
+  $RunHaplotypecaller.container       = "${params.repository}/sarek:${params.tag}"
   $RunManta.container                 = "${params.repository}/sarek:${params.tag}"
-  $RunMultiQC.container               = "${params.repository}/qctools:${params.tag}"
-  $RunMutect1.container               = "${params.repository}/mutect1:${params.tag}"
-  $RunMutect2.container               = "${params.repository}/gatk:${params.tag}"
+  $RunMultiQC.container               = "${params.repository}/sarek:${params.tag}"
+  $RunMutect2.container               = "${params.repository}/sarek:${params.tag}"
   $RunSamtoolsStats.container         = "${params.repository}/sarek:${params.tag}"
   $RunSingleManta.container           = "${params.repository}/sarek:${params.tag}"
   $RunSingleStrelka.container         = "${params.repository}/sarek:${params.tag}"
   $RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   $RunStrelka.container               = "${params.repository}/sarek:${params.tag}"
   $RunStrelkaBP.container             = "${params.repository}/sarek:${params.tag}"
-  $RunVcftools.container              = "${params.repository}/qctools:${params.tag}"
+  $RunVcftools.container              = "${params.repository}/sarek:${params.tag}"
   $RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
 }

configuration/genomes.config

@@ -42,6 +42,9 @@ params {
       knownIndels   = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       knownIndelsIndex = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
       snpeffDb      = "GRCh38.86"
+			// This a nasty-looking list of allele-frequencies files. Add/remove files to match to your sets
+			//AF_files			= "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf" 
+			//AF_indexes		= "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf.idx" 
     }
     'smallGRCh37' {
       acLoci      = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"

configuration/singularity-path.config

@@ -14,52 +14,50 @@ singularity {
 
 process {
   $BuildBWAindexes.container          = "${params.containerPath}/sarek-${params.tag}.img"
-  $BuildPicardIndex.container         = "${params.containerPath}/picard-${params.tag}.img"
+  $BuildReferenceIndex.container      = "${params.containerPath}/sarek-${params.tag}.img"
   $BuildSAMToolsIndex.container       = "${params.containerPath}/sarek-${params.tag}.img"
-  $BuildVCFIndex.container            = "${params.containerPath}/igvtools-${params.tag}.img"
+  $BuildVCFIndex.container            = "${params.containerPath}/sarek-${params.tag}.img"
   $CompressVCF.container              = "${params.containerPath}/sarek-${params.tag}.img"
   $ConcatVCF.container                = "${params.containerPath}/sarek-${params.tag}.img"
-  $CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
-  $GetVersionAll.container            = "${params.containerPath}/qctools-${params.tag}.img"
+  $CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionAll.container            = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionAlleleCount.container    = "${params.containerPath}/runallelecount-${params.tag}.img"
   $GetVersionASCAT.container          = "${params.containerPath}/r-base-${params.tag}.img"
-  $GetVersionBamQC.container          = "${params.containerPath}/qctools-${params.tag}.img"
+  $GetVersionBamQC.container          = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionBCFtools.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionBWAsamtools.container    = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionFastQC.container         = "${params.containerPath}/qctools-${params.tag}.img"
-  $GetVersionFreeBayes.container      = "${params.containerPath}/freebayes-${params.tag}.img"
-  $GetVersionGATK.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $GetVersionFastQC.container         = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionFreeBayes.container      = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionGATK.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionManta.container          = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionPicard.container         = "${params.containerPath}/picard-${params.tag}.img"
   $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   $GetVersionStrelka.container        = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionVCFtools.container       = "${params.containerPath}/qctools-${params.tag}.img"
+  $GetVersionVCFtools.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
-  $IndelRealigner.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $IndelRealigner.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $MapReads.container                 = "${params.containerPath}/sarek-${params.tag}.img"
-  $MarkDuplicates.container           = "${params.containerPath}/picard-${params.tag}.img"
+  $MarkDuplicates.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $MergeBams.container                = "${params.containerPath}/sarek-${params.tag}.img"
-  $RealignerTargetCreator.container   = "${params.containerPath}/gatk-${params.tag}.img"
-  $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $RealignerTargetCreator.container   = "${params.containerPath}/sarek-${params.tag}.img"
+  $RecalibrateBam.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
   $RunAscat.container                 = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunBamQC.container                 = "${params.containerPath}/qctools-${params.tag}.img"
+  $RunBamQC.container                 = "${params.containerPath}/sarek-${params.tag}.img"
   $RunBcftoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunConvertAlleleCounts.container   = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunFastQC.container                = "${params.containerPath}/qctools-${params.tag}.img"
-  $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
-  $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"
-  $RunHaplotypecaller.container       = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunFastQC.container                = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunFreeBayes.container             = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunGenotypeGVCFs.container         = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunHaplotypecaller.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $RunManta.container                 = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunMultiQC.container               = "${params.containerPath}/qctools-${params.tag}.img"
-  $RunMutect1.container               = "${params.containerPath}/mutect1-${params.tag}.img"
-  $RunMutect2.container               = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunMultiQC.container               = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunMutect2.container               = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSamtoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSingleManta.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSingleStrelka.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSnpeff.container                = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   $RunStrelka.container               = "${params.containerPath}/sarek-${params.tag}.img"
   $RunStrelkaBP.container             = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunVcftools.container              = "${params.containerPath}/qctools-${params.tag}.img"
+  $RunVcftools.container              = "${params.containerPath}/sarek-${params.tag}.img"
   $RunVEP.container                   = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
 }

configuration/uppmax-localhost.config

@@ -43,7 +43,7 @@ process {
   $BuildBWAindexes {
     memory = {params.totalMemory} // TODO This is likely too high
   }
-  $BuildPicardIndex {
+  $BuildReferenceIndex {
     memory = {params.totalMemory} // TODO This is likely too high
   }
   $BuildSAMToolsIndex {
@@ -70,7 +70,9 @@ process {
     memory = {params.totalMemory}
   }
   $MarkDuplicates {
-    memory = {params.singleCPUMem * 2 * task.attempt}
+		// Actually the -Xmx value should be kept lower  
+    cpus = 16
+    memory = {2 * params.singleCPUMem}
   }
   $MergeBams {
     cpus = 16
@@ -117,10 +119,6 @@ process {
   }
   $RunMultiQC {
   }
-  $RunMutect1 {
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-  }
   $RunMutect2 {
     cpus = 1
     memory = {params.singleCPUMem * task.attempt}