Closed jfy133 closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit fa8f6ef
+| ✅ 304 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 6 tests had warnings |!
Looks good with a couple of questions:
- Is it the new behaviour of
--input
that merits the 2.5.4 -> 3.0?- I saw a number of closed issues yesterday in emails, e.g. CheckM2 and dRep, but I don't see these changes included here.
- Fonts in the svg files appear different
Thanks @erikrikarddaniel !
To answer your questions:
--input '*{R1,R2}.fasta.gz
, I consider this a backwards incompatible change, so following semvar this would equate to an API breaking change I hope that answers your questions!
Regarding no 2: Since I just started a run and saw the closed issues, I had some hopes of finding those features in 3.0, giving me extra motivation to look at the PR 😉.
Regarding no 2: Since I just started a run and saw the closed issues, I had some hopes of finding those features in 3.0, giving me extra motivation to look at the PR 😉.
Aha, well one of them already has a module (checkm2 I think), so I promise to prioritise this for your review.😬
But highest priority now is adding nf-test so we can be sure we stop breaking things 😅
TODO:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).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).