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Merge pull request #673 from apeltzer/dev
Add Tuebingen specific configuration parameters
2 parents 5ef1dec + da914b2 commit 9c28a03

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‎CHANGELOG.md‎

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@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
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### `Added`
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- [#671](https://github.com/SciLifeLab/Sarek/pull/671) - New `publishDirMode` param and docs
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- [#673](https://github.com/SciLifeLab/Sarek/pull/673) - Profiles for BinAC and CFC clusters in Tübingen
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### `Changed`
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‎conf/binac.config‎

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}
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params {
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publishDirMode = 'symlink'
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max_memory = 128.GB
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max_cpus = 28
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max_time = 48.h

‎conf/cfc.config‎

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/*
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* -------------------------------------------------------------
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* Nextflow config file for use with Singularity on CFC at QBIC
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* -------------------------------------------------------------
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* Defines basic usage limits and singularity image id.
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*/
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/*
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*To be improved by process specific configuration asap, once our CFC cluster has the extra options removed - till then, task.attempt in NextFlow is not supported there.
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*/
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process {
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beforeScript = 'module load qbic/singularity_slurm/2.5.2'
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executor = 'slurm'
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}
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params {
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publishDirMode = 'symlink'
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max_memory = 60.GB
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max_cpus = 20
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max_time = 140.h
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}

‎conf/resources.config‎

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/*
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------
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* Generalized resource configuration for clusters
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* -------------------------------------------------
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*/
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params {
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singleCPUMem = 7.GB // for processes that are using more memory but a single CPU only. Use the 'core' queue for these
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}
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process {
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cpus = { check_max( 10, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
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maxErrors = '-1'
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maxRetries = 3
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withName:MapReads {
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memory = { check_max( 60.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 10, 'cpus' ) }
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}
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withName:CreateRecalibrationTable {
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cpus = { check_max( 12, 'cpus' ) }
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memory = {params.singleCPUMem * 8 * task.attempt}
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}
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withName:MarkDuplicates {
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// Actually the -Xmx value should be kept lower
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cpus = { check_max( 16, 'cpus' ) }
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memory = { check_max( 60.GB * task.attempt, 'memory' ) }
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}
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withName:MergeBams {
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memory = {params.singleCPUMem * task.attempt}
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RecalibrateBam {
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cpus = { check_max( 12, 'cpus' ) }
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memory = { check_max( 7.GB * 8 * task.attempt, 'memory' ) }
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunAlleleCount {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 14.GB * task.attempt, 'memory' ) }
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}
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withName:RunAscat {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 14.GB * task.attempt, 'memory' ) }
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}
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withName:RunBcftoolsStats {
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cpus = { check_max( 1, 'cpus' ) }
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}
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withName:RunConvertAlleleCounts {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 14.GB * task.attempt, 'memory' ) }
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}
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withName:RunFastQC {
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cpus = { check_max( 2, 'cpus' ) } // FastQC is only capable of running one thread per fastq file.
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errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
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}
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withName:RunFreeBayes {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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}
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withName:RunHaplotypecaller {
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cpus = { check_max( 20, 'cpus' ) }
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// Increase memory quadratically
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memory = { check_max( 7.GB * 2 * task.attempt, 'memory' ) }
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunGenotypeGVCFs {
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cpus = { check_max( 20, 'cpus' ) }
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memory = { check_max( 7.GB * task.attempt, 'memory' ) }
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}
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withName:RunMultiQC {
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errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
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}
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withName:RunMutect2 {
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cpus = { check_max( 2, 'cpus' ) }
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memory = { check_max( 7.GB * task.attempt, 'memory' ) }
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunSamtoolsStats {
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cpus = { check_max( 2, 'cpus' ) }
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunSingleStrelka {
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunSnpeff {
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cpus = { check_max( 1, 'cpus' ) }
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errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
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}
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withName:RunStrelka {
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cpus = { check_max( 1, 'cpus' ) }
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time = { check_max( 5.h * task.attempt, 'time' ) }
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}
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withName:RunVEP {
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cpus = { check_max( 1, 'cpus' ) }
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errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
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}
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}

‎nextflow.config‎

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includeConfig 'conf/base.config'
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includeConfig 'conf/binac.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/resources.config'
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includeConfig 'conf/containers.config'
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}
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// Default config for CFC cluster in Tuebingen/Germany
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cfc {
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includeConfig 'conf/base.config'
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includeConfig 'conf/cfc.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/resources.config'
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includeConfig 'conf/containers.config'
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}
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}

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