fix(umicollapse): locate installed jar independent of package build suffix - #12835
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…uffix UMICollapse is packaged with different build suffixes across the existing container and current Bioconda environment. Discover its jar within the active installation prefix instead of pinning the wrapper to a particular package build string.
process.shell already includes pipefail in nf-core pipelines, so the explicit set is unnecessary here. The jar-path resolution change alters the exact string embedded in each BAM's @pg CL header line without touching alignment records (stats/flagstat/idxstats/fastq outputs are unaffected), so the SAM-line snapshots for the two BAM-mode module tests and the dependent subworkflow's bam output need refreshing.
matthdsm
approved these changes
Aug 27, 2026
SPPearce
approved these changes
Aug 27, 2026
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Summary
Rationale
UMICollapse is packaged with different build suffixes in the existing container and current Bioconda environment. Discovering its jar within the active installation prefix supports both without pinning the wrapper to a particular package build.
Split out from #12662 (this is the uncontentious part; the UMI-tools random-seed change stays in that PR for separate discussion). An earlier revision of this PR also added
set -o pipefail, but nf-core pipelines already set that viaprocess.shell, so it was dropped as redundant here.Tests
CI-verified: module (
umicollapse single end test,umicollapse paired tests) and dependent subworkflow (bam_dedup_stats_samtools_umicollapse) snapshots refreshed against actual x64 docker/conda/singularity output. Only the SAM-line hashes moved (the jar-path string embedded in each BAM's header changes text without touching alignment records) - stats/flagstat/idxstats/fastq outputs are unchanged.