Change simple fasq_align_{aligner} subworkflows to fastq_align_dna
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- Dominant language
- Nextflow
- Stars
- 246
- Forks
- 184
- PR merge metrics
- No merged PRs in 30d
Description
Potentially we should switch from the individual fastq_align_{aligner} subworkflows to fastq_align_dna.
For reference see here: https://github.com/nf-core/modules/issues/11075
Potential to dos:
- Adding
chromaptofastq_align_dna - How do we want to deal with
star, we would need to discuss that.
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 reviewing the fastq_align_{aligner} and fastq_align_dna subworkflows, then read the referenced nf-core/modules issue #11075. Determine how chromap should be added and resolve the open design question around star. Done means the migration plan and resulting subworkflow changes are agreed and implemented.
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
- Needs clarification
- Newbie friendliness
- 35/100