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Merge pull request #359 from jfy133/fix-eva

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Remove -S /bin/bash in clusteroptions for EVA
This commit is contained in:
James A. Fellows Yates 2022-03-29 13:51:41 +02:00 committed by GitHub
commit 7cad02d327
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2 changed files with 71 additions and 71 deletions
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4
conf/eva.config
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@ -17,7 +17,7 @@ process {
executor = 'sge' executor = 'sge'
penv = 'smp' penv = 'smp'
queue = 'all.q' queue = 'all.q'
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" }
} }
executor { executor {
@ -37,7 +37,7 @@ profiles {
process { process {
queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' } queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
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" }
} }
singularity { singularity {

138
conf/pipeline/eager/eva.config
View file

@ -14,7 +14,7 @@ process {
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 = { "-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'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
@ -61,17 +61,17 @@ process {
// 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 = { "-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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: fastqc { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: adapter_removal { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
@ -92,95 +92,95 @@ process {
} }
withName: samtools_flagstat { 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 { 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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: markduplicates { 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' ) } 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 { 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 { 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 { 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' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
} }
withName: metagenomic_complexity_filter { 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 { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } clusterOptions = { "-V -l h_vmem=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 = { "-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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: multivcfanalyzer { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: mtnucratio { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: vcf2genome { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: qualimap { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
} }
withName: damageprofiler { 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' ) } 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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: circulargenerator { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: preseq { 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' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }
withName: genotyping_ug { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
@ -207,7 +207,7 @@ 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 = { "-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'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
@ -247,58 +247,58 @@ profiles {
// Fixes for SGE and Java incompatibility due to (and also some samtools?!) 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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: fastqc { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: adapter_removal { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: samtools_flagstat { 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 { 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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: markduplicates { 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' ) } memory = { check_max( 32.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 { 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 { 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 { 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' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
} }
withName: metagenomic_complexity_filter { 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 { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } clusterOptions = { "-V -l h_vmem=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' ) }
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' }
@ -309,53 +309,53 @@ profiles {
} }
withName: maltextract { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: multivcfanalyzer { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: mtnucratio { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: vcf2genome { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: qualimap { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
} }
withName: damageprofiler { 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' ) } memory = { check_max( 16.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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: circulargenerator { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: genotyping_ug { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: preseq { 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' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }
@ -381,7 +381,7 @@ 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 = { "-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'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
@ -421,50 +421,50 @@ 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 = { "-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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: fastqc { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: adapter_removal { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: samtools_flagstat { 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 { 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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: markduplicates { 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' ) } memory = { check_max( 48.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 { 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' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) }
} }
withName: seqtype_merge { 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 { 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' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) }
} }
@ -473,64 +473,64 @@ profiles {
} }
withName: metagenomic_complexity_filter { 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 { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" } clusterOptions = { "-V -l h_vmem=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' ) }
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: maltextract { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: multivcfanalyzer { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: mtnucratio { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: vcf2genome { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: qualimap { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
} }
withName: damageprofiler { 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' ) } memory = { check_max( 32.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 { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: circulargenerator { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: genotyping_ug { 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: preseq { 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' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }