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Merge branch 'master' into feat/hasta_update

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Ramprasad Neethiraj 2022-08-23 11:21:58 +02:00 committed by GitHub
commit 9182b55acc
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1 changed files with 8 additions and 2 deletions
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conf/pipeline/raredisease/hasta.config
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@ -10,7 +10,7 @@ process {
withLabel:'sentieon' { withLabel:'sentieon' {
beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
} }
withName: BCFTOOLS_VIEW { withName: 'BCFTOOLS_VIEW' {
if (params.genome == 'GRCh37') { 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 "' 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') { } else if (params.genome == 'GRCh38') {
@ -20,7 +20,13 @@ process {
enabled: false, enabled: false,
] ]
} }
// Java memory fixes
withName:'QUALIMAP_BAMQC' { withName:'QUALIMAP_BAMQC' {
ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" } 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" : ''}" }
}
} }