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change bcftools output format
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1 changed files with 2 additions and 2 deletions
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@ -15,9 +15,9 @@ process {
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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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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 "'
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} else if (params.genome == 'GRCh38') {
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ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
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ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
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}
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publishDir = [
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enabled: false,
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