mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Reintroduce bionode8, bump overhead for flagstat
This commit is contained in:
parent
06b40798c0
commit
e8252ad61c
1 changed files with 73 additions and 61 deletions
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@ -14,7 +14,7 @@ process {
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maxRetries = 2
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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cpus = { check_max( 1, 'cpus' ) }
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@ -61,83 +61,87 @@ process {
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// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
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// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
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withName: makeSeqDict {
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withName: makeSeqDict {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: fastqc {
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withName: fastqc {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: adapter_removal {
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withName: adapter_removal {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: samtools_flagstat {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: dedup {
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withName: dedup {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: markduplicates {
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withName: markduplicates {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: library_merge {
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withName: library_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: seqtype_merge {
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withName: seqtype_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: additional_library_merge {
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withName: additional_library_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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}
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withName: malt {
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withName: malt {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
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cpus = { check_max( 32, 'cpus' ) }
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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}
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}
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withName: maltextract {
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withName: maltextract {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: multivcfanalyzer {
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withName: multivcfanalyzer {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: mtnucratio {
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withName: mtnucratio {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: vcf2genome {
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withName: vcf2genome {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: qualimap {
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withName: qualimap {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: damageprofiler {
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withName: damageprofiler {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: circularmapper {
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withName: circularmapper {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: circulargenerator {
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withName: circulargenerator {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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withName: preseq {
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withName: preseq {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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}
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withName: genotyping_ug {
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withName: genotyping_ug {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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}
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}
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}
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@ -163,7 +167,7 @@ profiles {
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maxRetries = 2
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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cpus = { check_max( 1, 'cpus' ) }
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@ -207,43 +211,47 @@ profiles {
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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}
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// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
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// Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use
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withName: makeSeqDict {
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withName: makeSeqDict {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: fastqc {
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withName: fastqc {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: adapter_removal {
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withName: adapter_removal {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: samtools_flagstat {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: dedup {
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withName: dedup {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: markduplicates {
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withName: markduplicates {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: library_merge {
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withName: library_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: seqtype_merge {
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withName: seqtype_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: additional_library_merge {
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withName: additional_library_merge {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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}
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withName: malt {
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withName: malt {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
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cpus = { check_max( 32, 'cpus' ) }
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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}
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}
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@ -254,43 +262,43 @@ profiles {
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}
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}
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withName: maltextract {
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withName: maltextract {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: multivcfanalyzer {
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withName: multivcfanalyzer {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: mtnucratio {
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withName: mtnucratio {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: vcf2genome {
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withName: vcf2genome {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: qualimap {
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withName: qualimap {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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}
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withName: damageprofiler {
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withName: damageprofiler {
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clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: circularmapper {
|
withName: circularmapper {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: circulargenerator {
|
withName: circulargenerator {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: genotyping_ug {
|
withName: genotyping_ug {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: preseq {
|
withName: preseq {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
|
||||||
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -316,7 +324,7 @@ profiles {
|
||||||
maxRetries = 2
|
maxRetries = 2
|
||||||
|
|
||||||
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
|
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
|
||||||
|
|
||||||
withLabel:'sc_tiny'{
|
withLabel:'sc_tiny'{
|
||||||
cpus = { check_max( 1, 'cpus' ) }
|
cpus = { check_max( 1, 'cpus' ) }
|
||||||
|
@ -363,36 +371,40 @@ profiles {
|
||||||
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
|
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
|
||||||
|
|
||||||
withName: makeSeqDict {
|
withName: makeSeqDict {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: fastqc {
|
withName: fastqc {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: adapter_removal {
|
withName: adapter_removal {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: samtools_flagstat {
|
||||||
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: dedup {
|
withName: dedup {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: markduplicates {
|
withName: markduplicates {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: library_merge {
|
withName: library_merge {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: seqtype_merge {
|
withName: seqtype_merge {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: additional_library_merge {
|
withName: additional_library_merge {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -402,49 +414,49 @@ profiles {
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: malt {
|
withName: malt {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
||||||
cpus = { check_max( 32, 'cpus' ) }
|
cpus = { check_max( 32, 'cpus' ) }
|
||||||
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: maltextract {
|
withName: maltextract {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: multivcfanalyzer {
|
withName: multivcfanalyzer {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: mtnucratio {
|
withName: mtnucratio {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: vcf2genome {
|
withName: vcf2genome {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: qualimap {
|
withName: qualimap {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: damageprofiler {
|
withName: damageprofiler {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: circularmapper {
|
withName: circularmapper {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: circulargenerator {
|
withName: circulargenerator {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: genotyping_ug {
|
withName: genotyping_ug {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: preseq {
|
withName: preseq {
|
||||||
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
||||||
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
Loading…
Reference in a new issue