millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-25 01:19:54 +00:00
Code Issues Releases Packages Activity

Merge branch 'master' into feat/hasta_update

Browse source
This commit is contained in:
Ramprasad Neethiraj 2022-08-23 11:21:58 +02:00 committed by GitHub
commit 9182b55acc
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 8 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

10
conf/pipeline/raredisease/hasta.config
View file

@ -10,7 +10,7 @@ process {
withLabel:'sentieon' {
beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
}
withName: BCFTOOLS_VIEW {
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') {
@ -20,7 +20,13 @@ process {
enabled: false,
]
}
// Java memory fixes
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" : ''}" }
}
}