diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 19de6d3..dfa3542 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -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 = { "-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'{ cpus = { check_max( 1, 'cpus' ) } @@ -61,83 +61,87 @@ process { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: fastqc { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: adapter_removal { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } + withName: samtools_flagstat { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + } + withName: dedup { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: markduplicates { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: library_merge { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: seqtype_merge { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: additional_library_merge { - 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" } + clusterOptions = { "-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 = { "-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' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } } withName: maltextract { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: multivcfanalyzer { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: mtnucratio { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: vcf2genome { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: qualimap { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: damageprofiler { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circularmapper { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: circulargenerator { - 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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } withName: preseq { - 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" } + clusterOptions = { "-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 = { "-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" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } } } @@ -163,7 +167,7 @@ profiles { maxRetries = 2 // 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'{ cpus = { check_max( 1, 'cpus' ) } @@ -207,43 +211,47 @@ profiles { time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } } - // 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 (and also some samtools?!) using more memory than you tell it to use withName: makeSeqDict { - 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: fastqc { - 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: adapter_removal { - 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: samtools_flagstat { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } } withName: dedup { - 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: markduplicates { - 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: library_merge { - 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: seqtype_merge { - 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: additional_library_merge { - 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" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } 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' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } } @@ -254,43 +262,43 @@ profiles { } withName: maltextract { - 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: multivcfanalyzer { - 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: mtnucratio { - 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: vcf2genome { - 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: qualimap { - 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: damageprofiler { - 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 { - 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 { - 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 { - 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 { - 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' } } @@ -316,7 +324,7 @@ profiles { maxRetries = 2 // 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'{ 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 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 { - 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 { - 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 { - 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 { - 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 { - 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' ) } } 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 { - 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' ) } } @@ -402,49 +414,49 @@ profiles { } 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' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } } 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 { - 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 { - 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 { - 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 { - 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 { - 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 { - 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 { - 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 { - 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 { - 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' } }