Important! Template update for nf-core/tools v3.4.1 #299
Merged
chris-cheshire merged 37 commits intodevfrom Nov 18, 2025
Merged
Important! Template update for nf-core/tools v3.4.1 #299chris-cheshire merged 37 commits intodevfrom
chris-cheshire merged 37 commits intodevfrom
Conversation
I removed the merge marker comments after adding the pipeline specific default params and allowing for pipeline-specific custom profiles
Updated nf-core/cutandrun main.nf to comply with template version 3.3.1
|
pinin4fjords
approved these changes
Oct 21, 2025
Member
pinin4fjords
left a comment
pinin4fjords
left a comment
There was a problem hiding this comment.
You are the master of these things, nobody I trust more.
mirpedrol
approved these changes
Nov 3, 2025
Member
mirpedrol
left a comment
mirpedrol
left a comment
There was a problem hiding this comment.
Very nice work @maxulysse! This will be very useful 🥳
I have left some comments mainly regarding nf-test, I am a bit confused with what is done in this PR or what should be done in the future.
But overall looks very good!
Member
There was a problem hiding this comment.
should we keep this file until nf-test tests are implemented in the pipeline?
Member
Author
There was a problem hiding this comment.
I assumed tests are failing since I only restored partial functionality from the old check samplesheet script.
I'd rather we don't try to make this ci work, and try migrating the tests to nf-test directly
Member
There was a problem hiding this comment.
mostly for our future selves, have this resource configurations been moved somewhere else?
Member
Author
There was a problem hiding this comment.
yes, I moved all in base, I believe that's where it should sit
Member
There was a problem hiding this comment.
are the tests removed because nf-test is not implemented yet? should we keep them anyway if they don't break anything?
Member
Author
There was a problem hiding this comment.
these are coming from the modules repo, so no need to retest them in the pipeline
| main: | ||
|
|
||
| def caller_list = ['seacr', 'macs2'] | ||
| callers = params.peakcaller ? params.peakcaller.split(',').collect { it.trim().toLowerCase() } : ['seacr'] |
Member
There was a problem hiding this comment.
I see you moved defining callers here! So my previous comment about params.callers is outdated, but I think params.callers should be removed from modules.config
Member
Author
There was a problem hiding this comment.
Agreeing with you, but I tried to limit my changes in this single PR
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
6 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.
Replaces:
PR checklist
nf-core 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).