mirror of
https://github.com/MillironX/nf-configs.git
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Merge pull request #360 from jfy133/master
Re-add bash bin specification for EVA
This commit is contained in:
James A. Fellows Yates
GitHub
commit
f172cce8b2
2 changed files with 107 additions and 123 deletions
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@ -17,7 +17,7 @@ process {
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executor = 'sge'
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penv = 'smp'
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queue = 'all.q'
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clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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}
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executor {
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@ -37,7 +37,7 @@ profiles {
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process {
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queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
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clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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}
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singularity {
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@ -14,7 +14,7 @@ process {
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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@ -57,145 +57,129 @@ process {
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memory = { check_max( 256.GB * task.attempt, 'memory' ) }
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time = '365.d'
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}
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// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
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withName: makeSeqDict {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: fastqc {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: adapter_removal {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: bwa {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
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}
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withName: bwamem {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
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}
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withName: circularmapper {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
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}
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withName: bowtie2 {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
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}
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withName: samtools_flagstat {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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}
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withName: samtools_flagstat_after_filter {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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}
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withName: dedup {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: markduplicates {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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memory = { check_max( 20.GB * task.attempt, 'memory' ) }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: library_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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}
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withName: seqtype_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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}
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withName: additional_library_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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withName: metagenomic_complexity_filter {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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}
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withName: malt {
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clusterOptions = { "-V -l h_vmem=1000G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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}
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withName: maltextract {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: multivcfanalyzer {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: mtnucratio {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: vcf2genome {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: qualimap {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
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}
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withName: damageprofiler {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: circularmapper {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: circulargenerator {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: preseq {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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withName: genotyping_ug {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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}
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profiles {
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medium_data {
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs'
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}
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executor {
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queueSize = 8
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}
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@ -207,7 +191,7 @@ profiles {
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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@ -247,58 +231,58 @@ profiles {
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// Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use
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withName: makeSeqDict {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: fastqc {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: adapter_removal {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: samtools_flagstat {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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}
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withName: samtools_flagstat_after_filter {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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}
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withName: dedup {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: markduplicates {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: library_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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}
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withName: seqtype_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
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}
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withName: additional_library_merge {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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withName: metagenomic_complexity_filter {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
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}
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||||
|
||||
withName: malt {
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clusterOptions = { "-V -l h_vmem=1000G" }
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||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
|
||||
cpus = { check_max( 32, 'cpus' ) }
|
||||
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
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||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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||||
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@ -309,53 +293,53 @@ profiles {
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}
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withName: maltextract {
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||||
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' }
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}
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||||
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withName: multivcfanalyzer {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: mtnucratio {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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||||
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withName: vcf2genome {
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clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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||||
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||||
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.'
|
||||
|
|
|
|||
Loading…
Reference in a new issue