From 3d2a612b39f2ff7a42aae29d8ba80da4afa12a19 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 29 Mar 2022 12:48:37 +0200 Subject: [PATCH] Remove setting of bash in clusterOotions --- conf/pipeline/eager/eva.config | 138 ++++++++++++++++----------------- 1 file changed, 69 insertions(+), 69 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 0e48e69..9b2d12c 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 = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -61,110 +61,110 @@ 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=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: samtools_flagstat_after_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(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' } } withName: library_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: seqtype_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: additional_library_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: metagenomic_complexity_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } + clusterOptions = { "-V -l h_vmem=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } } withName: maltextract { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(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' } } withName: circularmapper { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(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=${(task.memory.toGiga() * 2)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } @@ -191,7 +191,7 @@ 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=${task.memory.toGiga()}G" } + clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -231,58 +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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: samtools_flagstat_after_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: seqtype_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: additional_library_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 4.GB * task.attempt, 'memory' ) } } withName: metagenomic_complexity_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } + clusterOptions = { "-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' } @@ -293,53 +293,53 @@ profiles { } withName: maltextract { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: genotyping_ug { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } @@ -365,7 +365,7 @@ 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=${task.memory.toGiga()}G" } + clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } @@ -405,50 +405,50 @@ profiles { // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use withName: makeSeqDict { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: samtools_flagstat_after_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: dedup { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } withName: seqtype_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: additional_library_merge { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 6.GB * task.attempt, 'memory' ) } } @@ -457,64 +457,64 @@ profiles { } withName: metagenomic_complexity_filter { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } } withName: malt { - clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } + clusterOptions = { "-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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: genotyping_ug { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } + clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } }