New module: motifmatchr/matchmotifs
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Description
Module
Add motifmatchr/matchmotifs.
Purpose
The component scans BED regions against a JASPAR-format position frequency matrix collection and a reference FASTA. It emits a sparse Matrix Market motif-match matrix plus explicit row and column mapping tables.
This provides a reusable, lightweight annotation step for chromVAR and other motif-based workflows while keeping motif scanning separate from downstream statistical analysis.
Software
- bioconductor-motifmatchr 1.32.0
- Public Biocontainers image: quay.io/biocontainers/bioconductor-motifmatchr:1.32.0--r45ha27e39d_0
Validation
- nf-core module lint: 53 passed, 0 failed
- Docker test and stub test passed with nf-test
I will submit the implementation from my fork.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the motifmatchr/matchmotifs module entry and the biocontainers motifmatchr:1.32.0 image. Review the stated nf-core module lint, Docker test, and stub test validation, then confirm the module scans the BED, JASPAR-format matrix, and FASTA inputs and emits the sparse matrix plus row and column mappings.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Clearly specified
- Newbie friendliness
- 35/100