nf-core / nf-core/variantbenchmarking
Port local modules to nf-core/modules
Open
Nobody has claimed this yet.
enhancement
low priority
- Dominant language
- Nextflow
- Stars
- 51
- Forks
- 31
- Avg merge
- 1d 22h
- Merged PRs (30d)
- 1
Description
Description of feature
- bcftools/reheader
- bcftools/rename
- bgzip/tabix
- sort_bed -> gnu/sort
-
subtract_vcf -> bcftools/isec(SV analyser output is not a VCF file ) - variant_extractor -> https://github.com/nf-core/modules/issues/9996
- reformat_header -> nf-core/gawk
- vcf_to_csv -> gatk4/variantstotable
- publish_processed_vcfs -> ideally deleted (TBD)
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
Review the remaining unchecked items and trace where the local modules are referenced in the workflow. Check the nf-core/modules replacements for vcf_to_csv and the status of publish_processed_vcfs; subtract_vcf is explicitly blocked because the output is not a VCF. Done means the viable local modules are ported and the unresolved items are documented or removed.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100