Maxime U Garcia

### The plan - One Step At A Time #### Errors - modules - [x] local - [ ] nf-core - need to pull in the new changes - [...

I'll re-work all error messages in a separate PR once I am happy with nft-utils _Originally posted by @maxulysse in https://github.com/nf-core/sarek/pull/1975#discussion_r2337093273_

WIP: Fix warning nf core lint and nextflow lint

3

Replaces fully https://github.com/nf-core/sarek/pull/1911 Overlaps a bit with #1912 Splitting this beast in: - https://github.com/nf-core/sarek/pull/1961 - https://github.com/nf-core/sarek/pull/1962 ## PR checklist - [ ] This comment contains a description of changes (with...

### Description of feature Using https://github.com/lukfor/nft-csv cf https://github.com/nf-core/fetchngs/blob/5cccb1cc57e547821aa1f3eb8b41601368f8e073/tests/default.nf.test#L35 for an example

simplify TEMPLATE with nf-core-utils 0.4.0

1

Need NXF_VER 25.10.0 ## PR checklist - [ ] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [ ] If you've fixed...

TEMPLATE - add trainling slash for pipelines_testdata_base_path

2

from @vagkaratzas > Would it be too much pain to put a slash at the end of pipelines_testdata_base_path in tests/nextflow.config, in the next template update? Currently it's different to the...

### Description of the bug It would be nice to have a warning, when a versions is emitted, a success if a topics versions is. And a failure when neither...

### Description of feature Both the modules repo and TEMPLATE use slightly different actions/workflows for common things, and they are slightly diverging more and more. https://github.com/nf-core/modules/tree/master/.github/actions https://github.com/nf-core/tools/tree/dev/nf_core/pipeline-template/.github/actions We have 2...

Add docker runOptions to fix default root ownership issues

4

I think we might need to add docker runOptions, this seems to be an issue. cf: https://nextflow.slack.com/archives/C02TH6KNBCN/p1741604416453299