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add beforescript for sentieon

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This commit is contained in:
Ramprasad Neethiraj 2022-04-22 11:03:09 +02:00
parent 3e3e2be04b
commit 447b3ee05d
1 changed files with 6 additions and 5 deletions
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11
conf/pipeline/raredisease/hasta.config
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@ -7,6 +7,12 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) } cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) }
} }
withLabel:'sentieon' {
beforeScript = { [
"export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)",
"export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
].join(";") }
}
withName: BCFTOOLS_VIEW { withName: BCFTOOLS_VIEW {
if (params.genome == 'GRCh37') { if (params.genome == 'GRCh37') {
ext.args = '--output-type v --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 v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
@ -20,8 +26,3 @@ process {
} }
params {
sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
}