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nf-core / metapep

From metagenomes to epitopes and beyond
https://nf-co.re/metapep
MIT License
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`INPUT_CHECK` subworkflow restructure #71

Closed tillenglert closed 1 year ago

tillenglert commented 1 year ago

Description of feature

I would suggest to use the module check_samplesheet.nf directly within the pipeline instead of using a sub workflow, which invokes the module without doing anything else with the data.

Another option would be to include lines: 89 to 188 https://github.com/nf-core/metapep/blob/572918f45a394f42743eb77309fa96a92b486f8f/workflows/metapep.nf#L89 in the subworkflow, giving it an actual purpose.

Still in either case we should rename the module check_samplesheet.nf to something more fitting and if we keep the sub workflow INPUT_CHECK we should also rename it to something like ampliseq (PARSE_INPUT).

I already have some typo/cleanup/structure branch, in which I add stuff I come across and would add these changes here, before doing a PR.

skrakau commented 1 year ago

I like the idea of moving the channel preparations to a subworklfow. Then one should also document it within the code which channels with which structure are the output. But why only until line 188?

tillenglert commented 1 year ago

Whups seems like I only scrolled until the first process, maybe we could also include until line 230? What would you suggest?

skrakau commented 1 year ago

Yes, 230 seems good :)