@Melina Klostermann I assume you are doing the

nf-core pipelines lint

, then I will tackle the leftover warnings in

nextflow lint

part

Yes. it is quite a bit. I hope I am not completely breaking it 😅

what kind of stuff is it saying?

So I created the 5 files that it needed: │ files_exist: File not found: .github/actions/get-shards/action.yml │ │ files_exist: File not found: .github/actions/nf-test/action.yml │ │ files_exist: File not found: .github/workflows/pr-comment.yml │ │ files_exist: File not found: docs/CONTRIBUTING.md │ │ files_exist: File not found: tests/default.nf.test

the nextflow warnings are also not all harmless but luckily I have working test locally so I wil do a PR only if it passes

But then also │ files_exist: File must be removed: lib/NfcoreTemplate.groovy │ │ files_exist: File must be removed: lib/Utils.groovy │ │ files_exist: File must be removed: lib/WorkflowMain.groovy │ │ files_exist: File must be removed: lib/WorkflowClipseq.groovy │ │ files_exist: File must be removed: pipeline_template.yml │ │ files_exist: File must be removed: lib/nfcore_external_java_deps.jar these need to be removed, becasue they are outdated, so I did that and tried to transfer to the new rules. (Or codex did it). SO I am runing the test now to see if that was ok

ah okay!! sounds good, thank you !

The good news is the test_full_small seems to be working also on our hpc and even using apptainer instead of docker :)

I also have apptainer on the cluster but did not get test_full_small to work 😅 I will rerun it once we merge more PRs 👍