Update nf-core modules to latest, and fix subsequent breaking subworkflow input signatures
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- Dominant language
- Nextflow
- Stars
- 230
- Forks
- 142
- Avg merge
- 13h 41m
- Merged PRs (30d)
- 1
Description
Breaking changes introduced by the update that need handling:
SAMTOOLS_STATS/SAMTOOLS_SORT: reference input changed from
[meta, fasta]→[meta, fasta, fai](2 → 3 elements)*_MARKDUPLICATES_PICARD: input arity changed (3 → 2)GFFREAD: input changed (1 → 2)
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 by locating the module and subworkflow definitions affected by the listed SAMTOOLS_STATS, SAMTOOLS_SORT, MARKDUPLICATES_PICARD, and GFFREAD input changes. Update their callers to match the new signatures and verify that the ATAC-seq workflow completes with those modules.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100