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Fix missing/wrong SENTIEON_DEDUP stub output #4632

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merged 6 commits into from
Jan 24, 2024
Merged

Fix missing/wrong SENTIEON_DEDUP stub output #4632

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0d66009
Fix missing/wrong sentieon dedup stub output files
alkc Dec 20, 2023
1d97ce1
Create bam/crai stub file
alkc Dec 20, 2023
058fa2c
Fix extra quotation mark x_x
alkc Dec 20, 2023
6b03a9b
Merge branch 'master' into fix-sentieon-dedup-stub
ramprasadn Jan 8, 2024
c83afa6
Merge branch 'master' into fix-sentieon-dedup-stub
jemten Jan 9, 2024
b6d92cc
Merge branch 'master' into fix-sentieon-dedup-stub
maxulysse Jan 24, 2024
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12 changes: 7 additions & 5 deletions modules/nf-core/sentieon/dedup/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -89,15 +89,17 @@ process SENTIEON_DEDUP {
} else {
fix_ld_library_path = ''
}

def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: ".cram" // The suffix should be either ".cram" or ".bam".
def metrics = task.ext.metrics ?: "${prefix}${suffix}.metrics"
"""
$fix_ld_library_path

touch ${prefix}.cram
touch ${prefix}.cram.crai
touch ${prefix}.metrics
touch ${prefix}.score
touch "${prefix}${suffix}"
touch "${prefix}${suffix}\$(echo ${suffix} | sed 's/m\$/i/')"
touch "${metrics}"
touch "${metrics}.multiqc.tsv"
touch "${prefix}.score"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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