PR for Release 2.4.0 #446
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PR for Release 2.4.0 #446
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Fix Umicollapse PE wrong method set
Replace local `blat` for nf-core `blat` in contaminant filter subworkflow
Updating nextflex branch
Co-authored-by: Louis LE NEZET <[email protected]>
Template update 3.0.1
Adress issues from review
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Tiny bugfixes
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Massive overhaul of the entire pipeline. Lots of bugfixes, stability improvements and general work on pipeline structure to be able to fix things in the future more easily. Tooling was refined, improved reporting / output structure and lots of local modules are now in nf-core/modules. See changelog for full details or the milestone https://github.com/nf-core/smrnaseq/milestone/10 that lists all things that were tackled here.
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).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).