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Add minibwa components - #225

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lazappi wants to merge 10 commits into
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feature/add-minibwa
Open

Add minibwa components#225
lazappi wants to merge 10 commits into
mainfrom
feature/add-minibwa

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@lazappi

@lazappi lazappi commented Jul 21, 2026

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Description

Add components for minibwa, the successor to bwa-mem:

  • minibwa_index: Create an index from a FASTA file
  • minibwa_map: Align reads using an index

Checklist 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:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

@lazappi
lazappi marked this pull request as ready for review July 21, 2026 12:43
@lazappi
lazappi requested a review from mdgrv July 27, 2026 12:38

@mdgrv mdgrv left a comment

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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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2 participants