millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-12-22 02:38:16 +00:00
Code Issues Releases Packages Activity

update conf

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

7
conf/pipeline/raredisease/hasta.config
View file

@ -10,13 +10,6 @@ process {
withLabel:'sentieon' {
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 {
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 "'