mirror of
https://github.com/MillironX/nf-configs.git
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32 lines
1.3 KiB
Text
32 lines
1.3 KiB
Text
process {
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withName:'PICARD_MARKDUPLICATES' {
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memory = { check_max( 90.GB * task.attempt, 'memory' ) }
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}
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withName:'DEEPVARIANT' {
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cpus = { check_max( 16 * task.attempt, 'cpus' ) }
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memory = { check_max( 80.GB * task.attempt, 'memory' ) }
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}
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withLabel:'sentieon' {
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beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
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}
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withName: 'BCFTOOLS_VIEW' {
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if (params.genome == 'GRCh37') {
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ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
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} else if (params.genome == 'GRCh38') {
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ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
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}
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publishDir = [
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enabled: false,
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]
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}
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// Java memory fixes
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withName:'QUALIMAP_BAMQC' {
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clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
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}
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withName:'PICARD_MARKDUPLICATES' {
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clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
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}
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}
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