mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-13 05:03:10 +00:00
32 lines
1.3 KiB
Text
32 lines
1.3 KiB
Text
process {
|
|
|
|
withName:'PICARD_MARKDUPLICATES' {
|
|
memory = { check_max( 90.GB * task.attempt, 'memory' ) }
|
|
}
|
|
withName:'DEEPVARIANT' {
|
|
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
|
|
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
|
|
}
|
|
withLabel:'sentieon' {
|
|
beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
|
|
}
|
|
withName: 'BCFTOOLS_VIEW' {
|
|
if (params.genome == 'GRCh37') {
|
|
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 "'
|
|
} else if (params.genome == 'GRCh38') {
|
|
ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
|
|
}
|
|
publishDir = [
|
|
enabled: false,
|
|
]
|
|
}
|
|
|
|
// Java memory fixes
|
|
withName:'QUALIMAP_BAMQC' {
|
|
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
|
|
}
|
|
withName:'PICARD_MARKDUPLICATES' {
|
|
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
|
|
}
|
|
|
|
}
|