Input naming conventions
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Description
Follow up to https://github.com/nf-core/modules/pull/1437#discussion_r834774713
We currently use reads for unaligned reads(fastq), and then bam for the aligned reads, but this doesn't cover cram, and sam.
It also doesn't cover things like when a bam or a bed file are possible.
I personally think input is a little too vague to name the variable as well.
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 discussion on pull request #1437, then inspect the module inputs that use reads, bam, or input. Done means agreeing on a naming convention that covers fastq, bam, cram, sam, and cases with multiple possible file types, and applying it where relevant; the issue names no files or tests.
Written by the indexing model from the issue text.
Assessment
- Domain
- developer-experience, tooling
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100