Another question: how can I lint and test local subworkflows? I do not manage to get

nf-core subworkflows

to see them, but the GitHub CI sees them and one of them crashes… • I want to create a snap for: https://github.com/nf-core/pairgenomealign/tree/master/subworkflows/local/fasta_bgzip_index_dict_samtools • because its absence (or a bug in the test file) crashes the pull request for template update: https://github.com/nf-core/pairgenomealign/actions/runs/16591339677/job/46927546339?pr=83

have you tried

nf-test test subworkflows/

?

Thanks! It created a snapshot that I just committed.

could it be related to the warning about the null value in the publishdir so that the snapshot doesn't see them? https://github.com/nf-core/pairgenomealign/actions/runs/16593039410/job/46933155704?pr=83#step:4:550

But why did it work locally?

shared a GIF

I found the reason: GitHub runs (rightly) the tests with the

--ci

option.

--ci                  Activates CI mode. Instead of automatically storing
                              a new snapshot as per usual, it will now fail the
                              test.