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Merge pull request #698 from MaxUlysse/BTB
Add configuration profile for munin
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| /* | ||
| * ------------------------------------------------- | ||
| * Nextflow config file for Sarek | ||
| * ------------------------------------------------- | ||
| * Configuration for running on munin | ||
| * ------------------------------------------------- | ||
| */ | ||
|
|
||
| env { | ||
| NXF_WORK="/scratch" | ||
| } | ||
|
|
||
| params { | ||
| genome_base = params.genome == 'GRCh37' ? '/btb/references/Homo_sapiens/GATK/GRCh37/' : params.genome == 'GRCh38' ? '/btb/references/Homo_sapiens/GATK/GRCh38/' : 'References/smallGRCh37' | ||
| singleCPUMem = 15.GB | ||
| totalMemory = 754.GB | ||
| } | ||
|
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| executor.$local.cpus = 48 | ||
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| process { | ||
| // Default process resources | ||
|
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| // A process may use one core, | ||
| cpus = 1 | ||
|
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| // 15 GB of memory, | ||
| memory = {params.singleCPUMem} | ||
|
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| // and 48 of them are allowed to be launched simultaneously. | ||
| maxForks = 48 | ||
|
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| errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'} | ||
| maxErrors = '-1' | ||
| maxRetries = 3 | ||
|
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| // These processes are defined in buildReferences.nf | ||
|
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| withName:BuildBWAindexes { | ||
| memory = {params.totalMemory} // TODO This is likely too high | ||
| } | ||
| withName:BuildReferenceIndex { | ||
| memory = {params.totalMemory} // TODO This is likely too high | ||
| } | ||
| withName:BuildSAMToolsIndex { | ||
| memory = {params.totalMemory} // TODO This is likely too high | ||
| } | ||
| withName:BuildVCFIndex { | ||
| memory = {params.totalMemory} // TODO This is likely too high | ||
| } | ||
|
|
||
| // These processes are defined in main.nf | ||
|
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| withName:ConcatVCF { | ||
| cpus = 8 | ||
| } | ||
| withName:CreateRecalibrationTable { | ||
| cpus = 16 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:MapReads { | ||
| cpus = 48 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:MarkDuplicates { | ||
| // Actually the -Xmx value should be kept lower | ||
| cpus = 16 | ||
| memory = {2 * params.singleCPUMem} | ||
| } | ||
| withName:MergeBams { | ||
| cpus = 8 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RecalibrateBam { | ||
| memory = {params.singleCPUMem * task.attempt} | ||
| } | ||
| withName:RunAlleleCount { | ||
| memory = {params.singleCPUMem * 2 * task.attempt} | ||
| } | ||
| withName:RunAscat { | ||
| memory = {params.singleCPUMem * 2 * task.attempt} | ||
| } | ||
| withName:RunBamQCmapped { | ||
| cpus = 16 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunBamQCrecalibrated { | ||
| cpus = 16 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunBcftoolsStats { | ||
| } | ||
| withName:RunConvertAlleleCounts { | ||
| memory = {params.singleCPUMem * 2 * task.attempt} | ||
| } | ||
| withName:RunFastQC { | ||
| cpus = 2 // FastQC is only capable of running one thread per fastq file. | ||
| errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} | ||
| } | ||
| withName:RunFreeBayes { | ||
| memory = {params.singleCPUMem * task.attempt} | ||
| } | ||
| withName:RunHaplotypecaller { | ||
| // Increase memory quadratically | ||
| memory = {params.singleCPUMem * task.attempt * task.attempt} | ||
| } | ||
| withName:RunGenotypeGVCFs { | ||
| } | ||
| withName:RunManta { | ||
| cpus = 48 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunMultiQC { | ||
| } | ||
| withName:RunMutect2 { | ||
| memory = {params.singleCPUMem * task.attempt} | ||
| } | ||
| withName:RunSamtoolsStats { | ||
| } | ||
| withName:RunSingleManta { | ||
| cpus = 48 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunSingleStrelka { | ||
| cpus = 48 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunSnpeff { | ||
| errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} | ||
| memory = {params.singleCPUMem * task.attempt} | ||
| } | ||
| withName:RunStrelka { | ||
| cpus = 48 | ||
| memory = {params.totalMemory} | ||
| } | ||
| withName:RunVEP { | ||
| cpus = 48 | ||
| errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} | ||
| } | ||
| } |
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