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🟡 Changes recommended
The new TSV output breaks the existing CSV contract and lacks content-level test coverage.
Review effort: Balanced
Findings: 1
Open (3)
What changed in this PR
Updates the Tasmanian mismatch-analysis stage to version 2.0.5.
Changes:
- Replaces the legacy samtools pipeline with the indexed-BAM CLI.
- Preserves mapping, base-quality, and flag filters.
- Updates dependency and version metadata.
| File | Description |
|---|---|
modules/tasmanian.nf |
Upgrades and invokes tasmanian-mismatch 2.0.5. |
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| --min-base-quality 20 \ | ||
| --min-map-quality 30 \ | ||
| -F 3840 \ | ||
| -o ${library}.tasmanian.csv |
| tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg | ||
| tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions | ||
| tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.5'), topic: versions |
| set +e | ||
| set +o pipefail | ||
| samtools view -q 30 -F 3840 ${bam} | head -n 2000000 | run_tasmanian -r ${genome_fa} > ${library}.tasmanian.csv | ||
| tasmanian-mismatch ${bam} ${genome_fa} \ |
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Bumps tasmanian-mismatch to 2.0.5, rebased onto current master so it includes the fix_paths merge (#76). seq-shepherd PR nebiolabs/seq-shepherd#544 points this submodule at this branch's commit (89beaf7); please merge with a merge commit (not squash) so that commit stays on master.
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