Closed kedhammar closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit b883059
+| ✅ 168 tests passed |+
!| ❗ 25 tests had warnings |!
Addresses #8
what's the usecase for clumpify again? Is it to produce more compressed fastqs or something else?
what's the usecase for clumpify again? Is it to produce more compressed fastqs or something else?
https://nf-co.re/modules/bbmap_clumpify
Main use case for us seems to be deduplication
I would say skip clumpify at this point and maybe give a try to run fastp inside the main.nf as well? It should be ran for any file so fairly similar to fastqc I would imagine?
fastp is used in nf-core/demultiplex, see here for inspiration: https://github.com/nf-core/demultiplex/blob/aa4d93673a4e04b1daf7b4bd71269d6054275534/workflows/demultiplex.nf#L199
This PR is a bit too broad in scope, so I'm closing it. Please see https://github.com/nf-core/seqinspector/issues/8 for inspiration.
PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).