Merged
Conversation
8cac5f2 to
cfd2d9f
Compare
prototaxites
approved these changes
Aug 26, 2025
Contributor
prototaxites
left a comment
There was a problem hiding this comment.
Looks great, thanks @dialvarezs! Always happy for the removal of extraneous processes where possible 😎
re: the genomad db, I think there are instructions on the GitHub repo in an issue to create a smaller test DB. So we could look there to try and sort it.
jfy133
approved these changes
Sep 5, 2025
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR updates all remaining nf-core modules, with the exception of
porechop-abi, which is being updated in PR #854.Aside from updating input channels where neccessary, the main changes are:
BCFTOOLS_VIEWinstead of being generated in a separate indexing step.test_single_endprofile now downloads the full geNomad database. The reduced version we were using is not compatible with the current geNomad version. As an improvement, we could consider creating an updated mini geNomad database.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).