mirror of
https://github.com/MillironX/nf-configs.git
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Merge pull request #265 from jfy133/eva-eager-subprofiles
eva/eager: Try new strategy for SGE and Java incompatibility
This commit is contained in:
James A. Fellows Yates
GitHub
commit
5c9896b687
1 changed files with 224 additions and 12 deletions
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@ -69,7 +69,7 @@ process {
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}
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withName: adapter_removal {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 5)}G,virtual_free=${(task.memory.toGiga() * 5)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: dedup {
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@ -77,11 +77,11 @@ process {
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}
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withName: markduplicates {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: library_merge {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: malt {
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@ -97,7 +97,7 @@ process {
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}
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withName: mtnucratio {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: vcf2genome {
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@ -105,11 +105,11 @@ process {
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}
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withName: qualimap {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: damageprofiler {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: circularmapper {
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@ -129,6 +129,145 @@ process {
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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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process {
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
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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 = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8, 'cpus' ) }
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memory = { check_max( 24.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 32, 'cpus' ) }
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memory = { check_max( 256.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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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 = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: fastqc {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: adapter_removal {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: dedup {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: markduplicates {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: library_merge {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: malt {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName:hostremoval_input_fastq {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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time = 1440.h
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}
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withName: maltextract {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: multivcfanalyzer {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: mtnucratio {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: vcf2genome {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: qualimap {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: damageprofiler {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: circularmapper {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: circulargenerator {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: preseq {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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}
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}
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big_data {
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params {
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@ -143,13 +282,12 @@ profiles {
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process {
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maxRetries = 2
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
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withName:hostremoval_input_fastq {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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time = 1440.h
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}
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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 = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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@ -192,6 +330,80 @@ profiles {
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memory = { check_max( 512.GB * task.attempt, 'memory' ) }
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
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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 = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: fastqc {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: adapter_removal {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: dedup {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: markduplicates {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: library_merge {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName:hostremoval_input_fastq {
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 32.GB * task.attempt, 'memory' ) }
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time = 1440.h
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}
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withName: malt {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: maltextract {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: multivcfanalyzer {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: mtnucratio {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: vcf2genome {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: qualimap {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: damageprofiler {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: circularmapper {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: circulargenerator {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: preseq {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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}
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}
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