Citation Flywheel

This page tracks the highest-return work for making DotMatch easy to cite, reuse, and recognize in external workflows. It is intentionally about adoption mechanics, not scientific claims. Public claims still need the evidence gates listed in docs/scientific-claims.md.

Priority Actions

Priority	Action	Done When
P0	Upstream official nf-core modules	A DotMatch module PR is merged into nf-core/modules, with tests, metadata, containers, and a workflow adoption record.
P0	Publish a MultiQC module	MultiQC automatically discovers DotMatch outputs without a custom config, renders core assignment metrics, and has a released package or upstream integration.
P1	Publish Galaxy and Snakemake wrappers	Reviewed wrappers are available outside this repository, with tiny fixtures and documented outputs.
P1	Generate run citation artifacts	Done in AssaySpec runs: each production run writes methods.md, CITATION.bib, and software_versions.yml beside summary and report outputs.
P1	Add copyable methods and citation UI	Workbench and generated HTML reports expose a single “Copy methods and citation” action backed by the generated methods artifact.
P1	Document external evaluations	Three to five independent labs, cores, or workflow maintainers approve public use records with scope notes.
P1	Maintain the workflow integration kit	Homepage audience routes, workflow handoffs, citation links, and public-use record rules stay aligned in docs/workflow-integration-kit.md.
P1	Maintain the workflow integration roadmap	docs/workflow-integration-roadmap.md, docs/workflow-integration-plan.json, and the homepage evaluation surface stay aligned.
P2	Publish a methods and benchmark preprint	The manuscript demonstrates speed and the consequences of ambiguity, unsafe rescue, and incorrect barcode windows.
P2	Maintain public use records	Approved independent examples are listed in docs/adopters/ and mirrored in the public docs.

Operating Rules

• Record external integrations in docs/workflow-adoption.json only after they are accepted, released, or published outside this repository.

• Add public use records only with approved wording and a public URL.

• Keep citation text generated from checked project metadata, not manually copied into each report surface.

• Treat ambiguity, unsafe rescue, shifted windows, and barcode-window mistakes as first-class methods details whenever they affect interpretation.

Existing Owners

• External workflow submission checklist: Workflow Submission Pack.

• Methods and citation language: Methods and Citation Template.

• Public use records: DotMatch Public Use Records.

• Evidence limits for public claims: DotMatch Evidence Notes.

Implementation Notes

The next implementation slice should avoid one-off text in reports. Prefer a small shared artifact writer that can be called by CLI commands, Workbench exports, workflow wrappers, and report generators. A complete run should emit:

• methods.md: copyable methods prose with DotMatch version, command, input semantics, edit-distance metric, radius, ambiguity policy, alphabet policy, extraction window, and relevant warnings.

• CITATION.bib: BibTeX generated from CITATION.cff, release DOI, and package version metadata.

• software_versions.yml: versions for DotMatch, Python package, native library, workflow wrapper, and any comparator or report tool used in the run.

The Workbench and HTML reports should copy the contents of methods.md plus the canonical citation entry instead of maintaining their own text templates.