Migrate CAT local modules to nf-core ones#799
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@nf-core-bot fix linting |
prototaxites
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Hi @dialvarezs, I don’t have time to run any tests at the moment but wanted to say this looks really good - just one little comment so far. I’ll try and take a more in depth look later next week!
d4straub
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I had a look and found it looks great I think! However, I had no time to run the pipeline, so I hesitate to give it an approval (and I am just getting used to mag again).
jfy133
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Looking good again @dialvarezs !
- Can you double check there is no change to the output structure, and thus no changes needed there (given you've added CATPACK_BINS`, I wonder if we should describe that there
Otherwise I don't think there is any major blockers from me here, other than maybe the missing SUMMARISE for CATPACK_BINS
Once the changes here are made I would like to do my own quick test and then I think we are good o go
Very clean PR, thank you again!
Co-authored-by: James A. Fellows Yates <[email protected]>
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@nf-core-bot fix linting |
jfy133
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LGTM now @dialvarezs ! Thank you very much, I think this will be really helpful!
If he has time maybe @prototaxites can have another look through (as he's given quite a few comments before), and then merge.
Co-authored-by: James A. Fellows Yates <[email protected]>
prototaxites
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Hi @dialvarezs, this looks great! Couple of small comments - the one about params passing is definitely optional and it might make sense to do as a single PR refactoring all pipeline inputs down the line.
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Future-proof thinking: Is it better to pass the DB into this subwf as a channel, rather than reading it direct from the params? In future, it looks like params will only be available in the entry workflow and need to be passed through as arguments.
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Yeah, I guess it makes more sense to update this across the entire pipeline in a single PR.
Could you open an issue to keep track of this change?
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Co-authored-by: Jim Downie <[email protected]>
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Thanks for the reviews, @jfy133, @prototaxites, @d4straub! |
Main changes:
Closes #611, #735.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).