seqkit replace incorrectly uses the '-i' flag
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Description
Have you checked the docs?
Description of the bug
The seqkit replace module incorrectly uses the -i flag, I think the intended usage was to specify the input (incorrect). The -i is --ignore-case. Seqkit uses positional argument to specify the input.
It should be removed from here:
https://github.com/nf-core/modules/blob/04dcc4dfcfe7170ec292d4c8d518a6fa9bcb59d5/modules/nf-core/seqkit/replace/main.nf#L33-L38
It's not the end of the word, but it may break some peoples code. It should however still be removed as case is important.
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
Open modules/nf-core/seqkit/replace/main.nf at the referenced command lines and compare the documented seqkit replace invocation with the current flags. Confirm how seqkit treats positional input and -i, then verify that the module no longer changes case-sensitive behavior. Done means the incorrect flag is removed from this module.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 76/100