GATK4 first round without MuTect1 and indel realignment

annotate.nf

@@ -73,23 +73,23 @@ vcfToAnnotate = Channel.create()
 vcfNotToAnnotate = Channel.create()
 
 if (annotateVCF == []) {
+// by default we annotate both germline and somatic results 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 {
@@ -346,7 +350,6 @@ 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

@@ -181,7 +181,6 @@ def defineContainersList(){
     'gatk',
     'gatk4',
     'igvtools',
-    'mutect1',
     'picard',
     'qctools',
     'r-base',
@@ -208,8 +207,7 @@ 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"

configuration/containers.config

@@ -11,50 +11,47 @@ process {
   $BuildBWAindexes.container          = "${params.repository}/sarek:${params.tag}"
   $BuildPicardIndex.container         = "${params.repository}/picard:${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"
+  $BuildPicardIndex.container         = "${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

@@ -117,10 +117,6 @@ process {
   }
   $RunMultiQC {
   }
-  $RunMutect1 {
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-  }
   $RunMutect2 {
     cpus = 1
     memory = {params.singleCPUMem * task.attempt}

configuration/uppmax-slurm.config

@@ -116,12 +116,6 @@ process {
   $RunMultiQC {
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }
-  $RunMutect1 {
-    queue = 'core'
-    time = {params.runTime * task.attempt}
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-  }
   $RunMutect2 {
     cpus = 1
     memory = {params.singleCPUMem * task.attempt}

containers/sarek/Dockerfile

@@ -1,18 +1,9 @@
-FROM debian:8.9
+FROM nfcore/base:latest
 
 LABEL \
-  author="Maxime Garcia" \
+  authors="Maxime.Gracia@scilifelab.se, Szilveszter.Juhos@scilifelab.se" \
   description="Image with tools used in Sarek" \
-  maintainer="maxime.garcia@scilifelab.se"
+  maintainers="Maxime.Gracia@scilifelab.se, Szilveszter.Juhos@scilifelab.se"
 
-# Export PATH
-ENV \
-  MANTA_INSTALL_PATH=/opt/manta \
-  PATH=/opt/bcftools/bin:/opt/htslib/bin:/opt/samtools/bin:$PATH \
-  STRELKA_INSTALL_PATH=/opt/strelka
-
-# Build container
-ADD \
-  build.sh /usr/bin/
-RUN \
-  build.sh
+COPY environment.yml /
+RUN conda env update -n root -f /environment.yml && conda clean -a

containers/sarek/environment.yml

@@ -0,0 +1,24 @@
+# You can use this file to create a conda environment for this pipeline:
+# conda env create -f environment.yml
+name: sarek-core
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+
+dependencies:
+  - bcftools=1.8
+  - bwa=0.7.17
+  - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
+  - fastqc=0.11.7
+  - freebayes=1.2.0
+  - gatk4=4.0.3.0
+  - htslib=1.7
+  - igvtools=2.3.93
+  - manta=1.3.0
+  - multiqc=1.5
+  - qualimap=2.2.2a
+  - samtools=1.8
+  - strelka=2.9.3
+  - vcfanno=0.2.8
+  - vcftools=0.1.15

containers/vcfanno/Dockerfile

@@ -0,0 +1,15 @@
+FROM nfcore/base:latest
+
+LABEL \
+  author="Szilveszter Juhos" \
+  description="vcfanno Image for Sarek" \
+  maintainer="szilveszter.juhos@scilifelab.se"
+
+COPY environment.yml /
+
+RUN \
+  conda env create -f /environment.yml && \
+  conda clean -a
+
+  # Export PATH
+ENV PATH /opt/conda/envs/sarek-vcfanno-2.0/bin:$PATH