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James Fellows Yates 2021-12-02 10:35:35 +01:00
parent 7a49a66b36
commit 06b40798c0
1 changed files with 60 additions and 60 deletions
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120
conf/pipeline/eager/eva.config
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@ -14,7 +14,7 @@ process {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -61,83 +61,83 @@ process {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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" }
}
}
@ -163,7 +163,7 @@ profiles {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -210,40 +210,40 @@ profiles {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
@ -254,43 +254,43 @@ profiles {
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
@ -316,7 +316,7 @@ profiles {
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -363,36 +363,36 @@ profiles {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
}
withName: seqtype_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: additional_library_merge {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
}
@ -402,49 +402,49 @@ profiles {
}
withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
clusterOptions = { "-l h=!bionode08.eva.mpg.de -S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}