From 6a4309d62c98add6c1ba7cabe22b19bf2180fe9a Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 15 Aug 2018 09:01:21 +0200 Subject: [PATCH 1/3] replace old depreciated syntax with withName: to close #600 --- configuration/containers.config | 90 ++++++++++++------------- configuration/singularity-path.config | 94 +++++++++++++-------------- configuration/uppmax-localhost.config | 62 +++++++++--------- configuration/uppmax-slurm.config | 62 +++++++++--------- 4 files changed, 154 insertions(+), 154 deletions(-) diff --git a/configuration/containers.config b/configuration/containers.config index 5639a291fa..c712f1ee3d 100644 --- a/configuration/containers.config +++ b/configuration/containers.config @@ -8,49 +8,49 @@ */ process { - $BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}" - $BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}" - $BuildSAMToolsIndex.container = "${params.repository}/sarek:${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}/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}/sarek:${params.tag}" - $GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}" - $GetVersionBWAsamtools.container = "${params.repository}/sarek:${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}" - $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} - $GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}" - $GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}" - $GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} - $MapReads.container = "${params.repository}/sarek:${params.tag}" - $MarkDuplicates.container = "${params.repository}/sarek:${params.tag}" - $MergeBams.container = "${params.repository}/sarek:${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}/sarek:${params.tag}" - $RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}" - $RunConvertAlleleCounts.container = "${params.repository}/r-base:${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}/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}/sarek:${params.tag}" - $RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} + withName:BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}" + withName:BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}" + withName:BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}" + withName:BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}" + withName:CompressVCF.container = "${params.repository}/sarek:${params.tag}" + withName:ConcatVCF.container = "${params.repository}/sarek:${params.tag}" + withName:CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionAll.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}" + withName:GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}" + withName:GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionGATK.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionManta.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} + withName:GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}" + withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} + withName:MapReads.container = "${params.repository}/sarek:${params.tag}" + withName:MarkDuplicates.container = "${params.repository}/sarek:${params.tag}" + withName:MergeBams.container = "${params.repository}/sarek:${params.tag}" + withName:RecalibrateBam.container = "${params.repository}/sarek:${params.tag}" + withName:RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}" + withName:RunAscat.container = "${params.repository}/r-base:${params.tag}" + withName:RunBamQC.container = "${params.repository}/sarek:${params.tag}" + withName:RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}" + withName:RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}" + withName:RunFastQC.container = "${params.repository}/sarek:${params.tag}" + withName:RunFreeBayes.container = "${params.repository}/sarek:${params.tag}" + withName:RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}" + withName:RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}" + withName:RunManta.container = "${params.repository}/sarek:${params.tag}" + withName:RunMultiQC.container = "${params.repository}/sarek:${params.tag}" + withName:RunMutect2.container = "${params.repository}/sarek:${params.tag}" + withName:RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}" + withName:RunSingleManta.container = "${params.repository}/sarek:${params.tag}" + withName:RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}" + withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} + withName:RunStrelka.container = "${params.repository}/sarek:${params.tag}" + withName:RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}" + withName:RunVcftools.container = "${params.repository}/sarek:${params.tag}" + withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} } diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config index 9b51a46318..4f8db8f242 100644 --- a/configuration/singularity-path.config +++ b/configuration/singularity-path.config @@ -13,51 +13,51 @@ singularity { } process { - $BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img" - $BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img" - $BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${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}/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}/sarek-${params.tag}.img" - $GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img" - $GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${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" - $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} - $GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" - $GetVersionVCFtools.container = "${params.containerPath}/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}/sarek-${params.tag}.img" - $MapReads.container = "${params.containerPath}/sarek-${params.tag}.img" - $MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img" - $MergeBams.container = "${params.containerPath}/sarek-${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}/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}/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}/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}/sarek-${params.tag}.img" - $RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} + withName:BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img" + withName:GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img" + withName:GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} + withName:GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} + withName:IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:MapReads.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img" + withName:RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img" + withName:RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img" + withName:RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunManta.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} + withName:RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img" + withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} } diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config index f5907f6181..4b0c928b73 100644 --- a/configuration/uppmax-localhost.config +++ b/configuration/uppmax-localhost.config @@ -40,108 +40,108 @@ process { // These processes are defined in buildReferences.nf - $BuildBWAindexes { +withName:BuildBWAindexes { memory = {params.totalMemory} // TODO This is likely too high } - $BuildReferenceIndex { + withName:BuildReferenceIndex { memory = {params.totalMemory} // TODO This is likely too high } - $BuildSAMToolsIndex { + withName:BuildSAMToolsIndex { memory = {params.totalMemory} // TODO This is likely too high } - $BuildVCFIndex { + withName:BuildVCFIndex { memory = {params.totalMemory} // TODO This is likely too high } // These processes are defined in main.nf - $ConcatVCF { +withName:ConcatVCF { cpus = 8 } - $CreateRecalibrationTable { + withName:CreateRecalibrationTable { cpus = 16 memory = {params.totalMemory} } - $IndelRealigner { + withName:IndelRealigner { memory = {params.singleCPUMem * 2 * task.attempt} } - $MapReads { + withName:MapReads { cpus = 16 memory = {params.totalMemory} } - $MarkDuplicates { - // Actually the -Xmx value should be kept lower + withName:MarkDuplicates { + // Actually the -Xmx value should be kept lower cpus = 16 memory = {2 * params.singleCPUMem} } - $MergeBams { + withName:MergeBams { cpus = 16 memory = {params.totalMemory} } - $RealignerTargetCreator { + withName:RealignerTargetCreator { cpus = 4 memory = {params.singleCPUMem * 4 * task.attempt} } - $RecalibrateBam { + withName:RecalibrateBam { memory = {params.singleCPUMem * task.attempt} } - $RunAlleleCount { + withName:RunAlleleCount { memory = {params.singleCPUMem * 2 * task.attempt} } - $RunAscat { + withName:RunAscat { memory = {params.singleCPUMem * 2 * task.attempt} } - $RunBamQC { + withName:RunBamQC { cpus = 16 memory = {params.totalMemory} } - $RunBcftoolsStats { + withName:RunBcftoolsStats { } - $RunConvertAlleleCounts { + withName:RunConvertAlleleCounts { memory = {params.singleCPUMem * 2 * task.attempt} } - $RunFastQC { + withName:RunFastQC { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } - $RunFreeBayes { + withName:RunFreeBayes { cpus = 1 memory = {params.singleCPUMem * task.attempt} } - $RunHaplotypecaller { + withName:RunHaplotypecaller { // Increase memory quadratically memory = {params.singleCPUMem * task.attempt * task.attempt} } - $RunGenotypeGVCFs { + withName:RunGenotypeGVCFs { } - $RunManta { + withName:RunManta { cpus = 16 memory = {params.totalMemory} } - $RunMultiQC { + withName:RunMultiQC { } - $RunMutect2 { + withName:RunMutect2 { cpus = 1 memory = {params.singleCPUMem * task.attempt} } - $RunSamtoolsStats { + withName:RunSamtoolsStats { } - $RunSingleManta { + withName:RunSingleManta { cpus = 16 memory = {params.totalMemory} } - $RunSingleStrelka { + withName:RunSingleStrelka { cpus = 16 memory = {params.totalMemory} } - $RunSnpeff { + withName:RunSnpeff { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} memory = {params.totalMemory} // TODO Does SnpEff really require that much? } - $RunStrelka { + withName:RunStrelka { cpus = 16 memory = {params.totalMemory} } - $RunVEP { + withName:RunVEP { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} memory = {params.totalMemory} // TODO Does VEP really require that much? } diff --git a/configuration/uppmax-slurm.config b/configuration/uppmax-slurm.config index 821a3855d8..3bed8321d6 100644 --- a/configuration/uppmax-slurm.config +++ b/configuration/uppmax-slurm.config @@ -25,118 +25,118 @@ process { maxErrors = '-1' maxRetries = 3 - $BuildBWAindexes { +withName:BuildBWAindexes { } - $BuildReferenceIndex { + withName:BuildReferenceIndex { } - $BuildSAMToolsIndex { + withName:BuildSAMToolsIndex { } - $BuildVCFIndex { + withName:BuildVCFIndex { } - $ConcatVCF { + withName:ConcatVCF { queue = 'core' } - $CreateRecalibrationTable { + withName:CreateRecalibrationTable { cpus = 10 memory = {params.singleCPUMem * 8 * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $IndelRealigner { + withName:IndelRealigner { cpus = 1 memory = {params.singleCPUMem * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $MapReads { + withName:MapReads { time = {params.runTime * task.attempt} } - $MarkDuplicates { - // Actually the -Xmx value should be kept lower + withName:MarkDuplicates { + // Actually the -Xmx value should be kept lower cpus = 16 memory = {2 * params.singleCPUMem} } - $MergeBams { + withName:MergeBams { memory = {params.singleCPUMem * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $RealignerTargetCreator { + withName:RealignerTargetCreator { time = {params.runTime * task.attempt} } - $RecalibrateBam { + withName:RecalibrateBam { cpus = 8 memory = {params.singleCPUMem * 8 * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $RunAlleleCount { + withName:RunAlleleCount { cpus = 1 memory = {params.singleCPUMem * 2 * task.attempt} queue = 'core' } - $RunAscat { + withName:RunAscat { cpus = 1 memory = {params.singleCPUMem * 2 * task.attempt} queue = 'core' } - $RunBamQC { + withName:RunBamQC { } - $RunBcftoolsStats { + withName:RunBcftoolsStats { cpus = 1 } - $RunConvertAlleleCounts { + withName:RunConvertAlleleCounts { cpus = 1 memory = {params.singleCPUMem * 2 * task.attempt} queue = 'core' } - $RunFastQC { + withName:RunFastQC { errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } } - $RunFreeBayes { + withName:RunFreeBayes { cpus = 1 memory = {params.singleCPUMem * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $RunHaplotypecaller { + withName:RunHaplotypecaller { cpus = 1 // Increase memory quadratically memory = {params.singleCPUMem * task.attempt * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $RunGenotypeGVCFs { + withName:RunGenotypeGVCFs { cpus = 1 memory = {params.singleCPUMem} } - $RunManta { + withName:RunManta { } - $RunMultiQC { + withName:RunMultiQC { errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } } - $RunMutect2 { + withName:RunMutect2 { cpus = 1 memory = {params.singleCPUMem * task.attempt} queue = 'core' time = {params.runTime * task.attempt} } - $RunSamtoolsStats { + withName:RunSamtoolsStats { cpus = 1 time = {params.runTime * task.attempt} } - $RunSingleManta { + withName:RunSingleManta { } - $RunSingleStrelka { + withName:RunSingleStrelka { time = {params.runTime * task.attempt} } - $RunSnpeff { + withName:RunSnpeff { errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } } - $RunStrelka { + withName:RunStrelka { time = {params.runTime * task.attempt} } - $RunVEP { + withName:RunVEP { cpus = 1 errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } } From c989afaf5dd59f613f55ac66fb3e428cf29d0f8d Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 15 Aug 2018 14:33:40 +0200 Subject: [PATCH 2/3] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5d39b1ae74..3697325be5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,6 +46,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG +- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace depreciated $name syntax with withName ### `Fixed` - [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath` From 293c610b6f276e9f913a787b3cc55d16fe05a842 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 15 Aug 2018 15:23:13 +0200 Subject: [PATCH 3/3] fix syntax --- configuration/containers.config | 180 ++++++++++++++++++------ configuration/singularity-path.config | 188 +++++++++++++++++++------- configuration/uppmax-localhost.config | 4 +- configuration/uppmax-slurm.config | 2 +- 4 files changed, 279 insertions(+), 95 deletions(-) diff --git a/configuration/containers.config b/configuration/containers.config index c712f1ee3d..f30784f48c 100644 --- a/configuration/containers.config +++ b/configuration/containers.config @@ -8,49 +8,139 @@ */ process { - withName:BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}" - withName:BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}" - withName:BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}" - withName:BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}" - withName:CompressVCF.container = "${params.repository}/sarek:${params.tag}" - withName:ConcatVCF.container = "${params.repository}/sarek:${params.tag}" - withName:CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionAll.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}" - withName:GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}" - withName:GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionGATK.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionManta.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} - withName:GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}" - withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} - withName:MapReads.container = "${params.repository}/sarek:${params.tag}" - withName:MarkDuplicates.container = "${params.repository}/sarek:${params.tag}" - withName:MergeBams.container = "${params.repository}/sarek:${params.tag}" - withName:RecalibrateBam.container = "${params.repository}/sarek:${params.tag}" - withName:RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}" - withName:RunAscat.container = "${params.repository}/r-base:${params.tag}" - withName:RunBamQC.container = "${params.repository}/sarek:${params.tag}" - withName:RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}" - withName:RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}" - withName:RunFastQC.container = "${params.repository}/sarek:${params.tag}" - withName:RunFreeBayes.container = "${params.repository}/sarek:${params.tag}" - withName:RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}" - withName:RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}" - withName:RunManta.container = "${params.repository}/sarek:${params.tag}" - withName:RunMultiQC.container = "${params.repository}/sarek:${params.tag}" - withName:RunMutect2.container = "${params.repository}/sarek:${params.tag}" - withName:RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}" - withName:RunSingleManta.container = "${params.repository}/sarek:${params.tag}" - withName:RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}" - withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} - withName:RunStrelka.container = "${params.repository}/sarek:${params.tag}" - withName:RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}" - withName:RunVcftools.container = "${params.repository}/sarek:${params.tag}" - withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} + withName:BuildBWAindexes { + container = "${params.repository}/sarek:${params.tag}" + } + withName:BuildReferenceIndex { + container = "${params.repository}/sarek:${params.tag}" + } + withName:BuildSAMToolsIndex { + container = "${params.repository}/sarek:${params.tag}" + } + withName:BuildVCFIndex { + container = "${params.repository}/sarek:${params.tag}" + } + withName:CompressVCF { + container = "${params.repository}/sarek:${params.tag}" + } + withName:ConcatVCF { + container = "${params.repository}/sarek:${params.tag}" + } + withName:CreateRecalibrationTable { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionAll { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionAlleleCount { + container = "${params.repository}/runallelecount:${params.tag}" + } + withName:GetVersionASCAT { + container = "${params.repository}/r-base:${params.tag}" + } + withName:GetVersionBamQC { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionBCFtools { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionBWAsamtools { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionFastQC { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionFreeBayes { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionGATK { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionManta { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionSnpeff { + container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} + } + withName:GetVersionStrelka { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionVCFtools { + container = "${params.repository}/sarek:${params.tag}" + } + withName:GetVersionVEP { + container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} + } + withName:MapReads { + container = "${params.repository}/sarek:${params.tag}" + } + withName:MarkDuplicates { + container = "${params.repository}/sarek:${params.tag}" + } + withName:MergeBams { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RecalibrateBam { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunAlleleCount { + container = "${params.repository}/runallelecount:${params.tag}" + } + withName:RunAscat { + container = "${params.repository}/r-base:${params.tag}" + } + withName:RunBamQC { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunBcftoolsStats { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunConvertAlleleCounts { + container = "${params.repository}/r-base:${params.tag}" + } + withName:RunFastQC { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunFreeBayes { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunGenotypeGVCFs { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunHaplotypecaller { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunManta { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunMultiQC { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunMutect2 { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunSamtoolsStats { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunSingleManta { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunSingleStrelka { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunSnpeff { + container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} + } + withName:RunStrelka { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunStrelkaBP { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunVcftools { + container = "${params.repository}/sarek:${params.tag}" + } + withName:RunVEP { + container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} + } } diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config index 4f8db8f242..a8e1473191 100644 --- a/configuration/singularity-path.config +++ b/configuration/singularity-path.config @@ -13,51 +13,145 @@ singularity { } process { - withName:BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img" - withName:GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img" - withName:GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} - withName:GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} - withName:IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:MapReads.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img" - withName:RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img" - withName:RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img" - withName:RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunManta.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} - withName:RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img" - withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} + withName:BuildBWAindexes { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:BuildReferenceIndex { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:BuildSAMToolsIndex { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:BuildVCFIndex { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:CompressVCF { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:ConcatVCF { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:CreateRecalibrationTable { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionAll { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionAlleleCount { + container = "${params.containerPath}/runallelecount-${params.tag}.img" + } + withName:GetVersionASCAT { + container = "${params.containerPath}/r-base-${params.tag}.img" + } + withName:GetVersionBamQC { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionBCFtools { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionBWAsamtools { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionFastQC { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionFreeBayes { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionGATK { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionManta { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionSnpeff { + container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} + } + withName:GetVersionStrelka { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionVCFtools { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:GetVersionVEP { + container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} + } + withName:IndelRealigner { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:MapReads { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:MarkDuplicates { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:MergeBams { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RealignerTargetCreator { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RecalibrateBam { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunAlleleCount { + container = "${params.containerPath}/runallelecount-${params.tag}.img" + } + withName:RunAscat { + container = "${params.containerPath}/r-base-${params.tag}.img" + } + withName:RunBamQC { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunBcftoolsStats { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunConvertAlleleCounts { + container = "${params.containerPath}/r-base-${params.tag}.img" + } + withName:RunFastQC { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunFreeBayes { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunGenotypeGVCFs { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunHaplotypecaller { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunManta { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunMultiQC { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunMutect2 { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunSamtoolsStats { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunSingleManta { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunSingleStrelka { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunSnpeff { + container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"} + } + withName:RunStrelka { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunStrelkaBP { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunVcftools { + container = "${params.containerPath}/sarek-${params.tag}.img" + } + withName:RunVEP { + container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"} + } } diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config index 4b0c928b73..0ccef7e880 100644 --- a/configuration/uppmax-localhost.config +++ b/configuration/uppmax-localhost.config @@ -40,7 +40,7 @@ process { // These processes are defined in buildReferences.nf -withName:BuildBWAindexes { + withName:BuildBWAindexes { memory = {params.totalMemory} // TODO This is likely too high } withName:BuildReferenceIndex { @@ -55,7 +55,7 @@ withName:BuildBWAindexes { // These processes are defined in main.nf -withName:ConcatVCF { + withName:ConcatVCF { cpus = 8 } withName:CreateRecalibrationTable { diff --git a/configuration/uppmax-slurm.config b/configuration/uppmax-slurm.config index 3bed8321d6..a3ff07a0ca 100644 --- a/configuration/uppmax-slurm.config +++ b/configuration/uppmax-slurm.config @@ -25,7 +25,7 @@ process { maxErrors = '-1' maxRetries = 3 -withName:BuildBWAindexes { + withName:BuildBWAindexes { } withName:BuildReferenceIndex { }