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add beforescript for sentieon
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1 changed files with 6 additions and 5 deletions
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@ -7,6 +7,12 @@ process {
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cpus = { check_max( 16 * task.attempt, 'cpus' ) }
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memory = { check_max( 80.GB * task.attempt, 'memory' ) }
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}
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withLabel:'sentieon' {
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beforeScript = { [
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"export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)",
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"export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
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].join(";") }
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}
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withName: BCFTOOLS_VIEW {
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if (params.genome == 'GRCh37') {
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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 "'
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@ -20,8 +26,3 @@ process {
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}
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params {
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sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin"
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}
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