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New module: motifmatchr/matchmotifs - #12927

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PFRoux wants to merge 4 commits into
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PFRoux:add-motifmatchr-matchmotifs
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New module: motifmatchr/matchmotifs#12927
PFRoux wants to merge 4 commits into
nf-core:masterfrom
PFRoux:add-motifmatchr-matchmotifs

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@PFRoux

@PFRoux PFRoux commented Sep 10, 2026

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PR checklist

Closes #12926

Summary

Adds motifmatchr/matchmotifs for matching a JASPAR-format motif collection to BED regions using a reference FASTA.

The module emits:

  • a sparse Matrix Market motif-match matrix
  • a row mapping table for genomic regions
  • a column mapping table for motif identifiers

This deliberately keeps motif scanning separate from chromVAR deviation analysis, making the result reusable and avoiding a combined container with unrelated dependencies.

Software requirements

  • bioconda::bioconductor-motifmatchr=1.32.0
  • quay.io/biocontainers/bioconductor-motifmatchr:1.32.0--r45ha27e39d_0

Validation

  • nf-core modules lint motifmatchr/matchmotifs: 53 passed, 0 failed
  • nf-test with Docker: real execution and stub execution passed

Note: the Galaxy Singularity mirror for this exact newly published Biocontainers tag currently returns 404. The Docker/OCI image is public and was used for the test.

@PFRoux
PFRoux enabled auto-merge September 11, 2026 15:51
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New module: motifmatchr/matchmotifs

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