From 2277b541a3c40cd7713e28b002b69a05d6d9ae9d Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 31 Mar 2022 11:06:53 +0200 Subject: [PATCH] Re-add bash bin specification --- conf/eva.config | 4 +- conf/pipeline/eager/eva.config | 226 +++++++++++++++------------------ 2 files changed, 107 insertions(+), 123 deletions(-) diff --git a/conf/eva.config b/conf/eva.config index 428750e..866cdd5 100644 --- a/conf/eva.config +++ b/conf/eva.config @@ -17,7 +17,7 @@ process { executor = 'sge' penv = 'smp' queue = 'all.q' - clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } } executor { @@ -37,7 +37,7 @@ profiles { process { queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' } - clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } } singularity { diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index c2b3967..1eefd18 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 = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -57,145 +57,129 @@ process { memory = { check_max( 256.GB * task.attempt, 'memory' ) } time = '365.d' } - + // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - - withName: bwa { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } - } - - withName: bwamem { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } - } - - withName: circularmapper { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } - } - - withName: bowtie2 { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } - } withName: samtools_flagstat { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } - + withName: samtools_flagstat_after_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: dedup { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 20.GB * task.attempt, 'memory' ) } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: seqtype_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } - + withName: additional_library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } - + withName: metagenomic_complexity_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: malt { - clusterOptions = { "-V -l h_vmem=1000G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } } withName: maltextract { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' } } withName: damageprofiler { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } - + withName: genotyping_ug { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } } profiles { - + medium_data { - + params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs' } - + executor { queueSize = 8 } @@ -207,7 +191,7 @@ profiles { maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion - clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -247,58 +231,58 @@ profiles { // Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } - + withName: samtools_flagstat_after_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: dedup { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 32.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: seqtype_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: additional_library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: metagenomic_complexity_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: malt { - clusterOptions = { "-V -l h_vmem=1000G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } @@ -309,53 +293,53 @@ profiles { } withName: maltextract { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' } } withName: damageprofiler { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 16.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: genotyping_ug { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } @@ -363,13 +347,13 @@ profiles { } big_data { - + params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs' } - + executor { queueSize = 6 } @@ -381,7 +365,7 @@ profiles { maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion - clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -421,50 +405,50 @@ profiles { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } - + withName: samtools_flagstat_after_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: dedup { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 48.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName: seqtype_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: additional_library_merge { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } @@ -473,70 +457,70 @@ profiles { } withName: metagenomic_complexity_filter { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: malt { - clusterOptions = { "-V -l h_vmem=1000G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: maltextract { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' } } withName: damageprofiler { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } - memory = { check_max( 32.GB * task.attempt, 'memory' ) } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + memory = { check_max( 32.GB * task.attempt, 'memory' ) } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: genotyping_ug { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: preseq { - clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } } } - + pathogen_loose { params { config_profile_description = 'Pathogen (loose) MPI-EVA profile, provided by nf-core/configs.'