mirror of
https://github.com/MillironX/nf-configs.git
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505 lines
19 KiB
Text
505 lines
19 KiB
Text
// Profile config names for nf-core/configs
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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 EVA profile provided by nf-core/configs'
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}
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// Specific nf-core/eager process configuration
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process {
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
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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 -V -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.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( 4.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( 8.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( 4.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( 8.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( 16.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 -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: fastqc {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: adapter_removal {
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clusterOptions = { "-S /bin/bash -V -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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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: markduplicates {
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clusterOptions = { "-S /bin/bash -V -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 -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: seqtype_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: additional_library_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(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: malt {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: multivcfanalyzer {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: mtnucratio {
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clusterOptions = { "-S /bin/bash -V -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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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: qualimap {
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clusterOptions = { "-S /bin/bash -V -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 -V -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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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: circulargenerator {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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}
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withName: preseq {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(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 = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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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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process {
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
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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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: seqtype_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: additional_library_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(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: malt {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=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:hostremoval_input_fastq {
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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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
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}
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withName: genotyping_ug {
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clusterOptions = { "-S /bin/bash -V -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 -V -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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// 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 big-data EVA profile provided by nf-core/configs'
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}
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executor {
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queueSize = 6
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}
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process {
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
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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 -V -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( 2.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( 8.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( 16.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( 8.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( 16.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( 32.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( 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 -V -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 -V -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 -V -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 -V -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 -V -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 -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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}
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withName: seqtype_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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}
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withName: additional_library_merge {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName:hostremoval_input_fastq {
|
|
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
|
|
time = 1440.h
|
|
}
|
|
|
|
withName: malt {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
|
|
cpus = { check_max( 32, 'cpus' ) }
|
|
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
|
|
}
|
|
|
|
withName: maltextract {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: multivcfanalyzer {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: mtnucratio {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: vcf2genome {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: qualimap {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: damageprofiler {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: circularmapper {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: circulargenerator {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: genotyping_ug {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
|
|
}
|
|
|
|
withName: preseq {
|
|
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(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.'
|
|
bwaalnn = 0.01
|
|
bwaalnl = 16
|
|
}
|
|
}
|
|
pathogen_strict {
|
|
params {
|
|
config_profile_description = 'Pathogen (strict) MPI-EVA SDAG profile, provided by nf-core/configs.'
|
|
bwaalnn = 0.1
|
|
bwaalnl = 32
|
|
}
|
|
}
|
|
human {
|
|
params {
|
|
config_profile_description = 'Human MPI-EVA SDAG profile, provided by nf-core/configs.'
|
|
bwaalnn = 0.01
|
|
bwaalnl = 16500
|
|
}
|
|
}
|
|
1240k {
|
|
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
|
|
}
|
|
|
|
process {
|
|
|
|
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
|
|
|
|
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=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
|
|
|
|
// Increasing walltime for bwa to avoid unnecessary retries
|
|
withName:bwa {
|
|
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 72.h : 48.h }
|
|
}
|
|
|
|
withName:markduplicates {
|
|
memory = { task.attempt == 3 ? 16.GB : task.attempt == 2 ? 8.GB : 4.GB }
|
|
}
|
|
}
|
|
}
|
|
}
|