Adding a field for custom params for STAR
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Description
Description of feature
Hello,
This enhancement request is related to #81 .
I was wondering if a parameter might be added such as " --extra_star_align_args" that does the same as in the rnaseq pipeline from nfcore.
I often need to set several custom params for alignment and an option to do so would be nice.
Alternatively, perhaps a "--skip_alignment" param so that a user might run STAR on its own but then continue with the rest of the workflow.
If what I'm describing is already relatively straightforward, apologies, how might this use-case be accomplished?
Thanks!
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Research direction
No file, test, or entry point is named. Start by reviewing related issue #81 and the nf-core RNA-seq pipeline behavior referenced here; clarify whether the desired outcome is configurable STAR alignment arguments, a skip-alignment option, or both, then define how the workflow continues and how each option is verified.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100