Restructure local modules and subworkflows#851
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prototaxites
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Hi @dialvarezs, this looks really good!
Haven't had a chance to go through with a fine-tooth comb yet, but a couple of thoughts after a quick consideration:
jfy133
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Really good job again @dialvarezs ! Only a few things
My main grip is the over-nesting of everything, but I am conflicting with Jim on that one. Maybe you can bring this up on slack for a 'style' discussion before reducing the number of nesting (and sorry about that!)
Btw once this is in, I will fix all the missing versions that I just noticed there is a linting for 🙃 but then we will have got rid a lot of the linting errors 🎉
Co-authored-by: James A. Fellows Yates <[email protected]>
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So, by popular decision I flattened everything. I also fixed the input channel rewrites. I've added the meta files for the subworkflows too, so we can get rid of those warnigs. I also was considering updating the modules to tackle a few more warnings, but I guess it would be too much for this PR. I'll save that for the next one. Ready for a next review round. |
jfy133
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Oh wow @dialvarezs you even added all the meta.yamls swoon!!! Thank you!
I only did a very cursory glance of them as a I'm a bit low on time and I think we should get this ASAP, but also they are not specifically used for anything at the moment - so any mistakes we can fix over time.
Otherwise I looked through change suggestions from before and everything is addressed I think, this LGTM to me now!
I agree don't worry about module updates for now - this is turning into a bit of a monster PR and these aren't really 'fixes' for anything
@prototaxites otherwise everything look good to you now?
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Have also only had a brief glance over, but generally happy with it and I think we can shake out residual issues in a new PR! |
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Can we get a nice fat shiny green ✔️ @prototaxites ? |
Summary
POOL_*modules and useCAT_FASTQinsteadch_*, add prefix unused variables with underscores.Closes #810 #817
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).