Add minibwa components - #225
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lazappi
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July 21, 2026 12:43
mdgrv
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Both components look clean and behave well on real data.
Checked:
- viash ns test -q minibwa → all 4 build+test SUCCESS; ASCII build gate passes (matches CI).
- Configs follow the 0.9.x conventions (engines/runners/argument_groups, boolean_true flags, meta_cpus, pinned minibwa:0.4--hab16a5f_0 with software_versions.txt), and the arg groups map cleanly onto the minibwa index / minibwa map CLI.
- Real-run smoke test on a SEQC2 HCC1395 chr21 ~30x tumor pair (~6.27M reads): index built fine, and minibwa_map gave 99.03% mapped / 97.90% properly paired, vs bwa_mem 99.57% / 98.96% on the same reads; within ~1 pp on every flagstat metric and noticeably faster. SAM header is correct (@SQ/@RG/@pg all present).
Note:
- In minibwa_map/script.sh the index prefix is resolved via ls "${par_index%/}"/*.l2b, if a dir ever holds more than one .l2b it silently picks one.
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Description
Add components for
minibwa, the successor tobwa-mem:minibwa_index: Create an index from a FASTA fileminibwa_map: Align reads using an indexChecklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: