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update conf

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This commit is contained in:
Ramprasad Neethiraj 2022-08-18 15:56:41 +02:00
parent 1c942759ea
commit dd63dee7aa
1 changed files with 0 additions and 7 deletions
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conf/pipeline/raredisease/hasta.config
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@ -10,13 +10,6 @@ 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" }
} }
// 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" : ''}" }
}
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 "'