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feat: support task.ext.args in sentieon/gvcftyper #11763

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feat: support task.ext.args in sentieon/gvcftyper #11763

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feat: support task.ext.args in sentieon/gvcftyper
nicorap May 26, 2026
2d5a9eb
Merge branch 'master' into feat/sentieon-gvcftyper-ext-args
SPPearce May 26, 2026
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2 changes: 2 additions & 0 deletions modules/nf-core/sentieon/gvcftyper/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ process SENTIEON_GVCFTYPER {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_genotyped"
def gvcfs_input = '-v ' + gvcfs.join(' -v ')
def dbsnp_cmd = dbsnp ? "--dbsnp ${dbsnp}" : ""
Expand All @@ -38,6 +39,7 @@ process SENTIEON_GVCFTYPER {
-r ${fasta} \\
${interval_command} \\
--algo GVCFtyper \\
${args} \\
${gvcfs_input} \\
${dbsnp_cmd} \\
${prefix}.vcf.gz
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