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add DotMatch modules#12156

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dnncha wants to merge 1 commit into
nf-core:masterfrom
dnncha:codex/add-dotmatch-modules
Draft

add DotMatch modules#12156
dnncha wants to merge 1 commit into
nf-core:masterfrom
dnncha:codex/add-dotmatch-modules

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@dnncha

@dnncha dnncha commented Jun 23, 2026

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What this adds

Adds nf-core module candidates for DotMatch 0.1.8:

  • dotmatch/count
  • dotmatch/crispr_count
  • dotmatch/demux
  • dotmatch/audit
  • dotmatch/panel_check
  • dotmatch/assay_run

Each module includes main.nf, meta.yml, an environment.yml pinned to bioconda::dotmatch=0.1.8, and tiny nf-test fixtures copied from the DotMatch repository workflow examples.

Why

DotMatch provides deterministic fixed-window known-target short-DNA assignment for CRISPR guides, inline barcodes, panel checks, and related QC workflows. The module set is intended to make the tool easier to adopt from nf-core pipelines while preserving explicit unique, ambiguous, none, and invalid assignment semantics.

Validation

  • DotMatch source repository gates passed before preparing this branch: make repository-ready, make test, make workflow-examples-ready, make assay-evidence-ready, make scientific-readiness-ready, make barcode-comparison-gate, make native-exact-gate, make distribution-record-ready, make bioconda-recipe-ready, and make joss-paper-ready.
  • PyPI, Bioconda, GHCR manifest, and Zenodo distribution checks pass for DotMatch 0.1.8 in the source repository.
  • I could not run nf-core modules lint or nf-test locally because this workstation does not have Java/Nextflow installed. I installed nf-core in an isolated venv and confirmed lint stops on missing nextflow before module-specific checks.

Review notes

This is opened as a draft because upstream maintainers may prefer splitting the six DotMatch subcommands into separate PRs and may want regenerated nf-test snapshots under the current nf-core tooling.

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