As I mentioned above, I'm converting #C04NLA7QHH9 to nf-test pipeline tests. When making the PR, linting fails:

actions_ci: Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'

I had copied and modified the file from #CEA7TBJGJ and I also checked the corresponding file in some other pipelines. #C02K5GX2W93 is very similar, with the Nextflow version only mentioned in this block:

jobs:
  define_nxf_versions:
    name: Choose nextflow versions to test against depending on target branch
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.nxf_versions.outputs.matrix }}
    steps:
      - id: nxf_versions
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
          else
            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
          fi

(The above is #C04NLA7QHH9, #C02K5GX2W93 differs only in having "23.10.0".) #CE9MS66BS and #CE8SSJV3N have quite different files, at least superficially. My questions: 1) How and where should the NF version be tested? 2) Which pipeline (and branch) is good to use as a template for nf-test conversion?

I'd say #CE8SSJV3N dev branch is the one to go for, since we're about to release

And you're passing linting? 🙂

of course

You have this:

NXF_VER:
          - "latest-everything"
          - "23.04"

where I (and #CEA7TBJGJ and #C02K5GX2W93) have:

NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}

This is the only mention of NF version I see in your file. Changing mine to your version, doesn't pass linting anyway.

NXF_VER

is referenced in three identical places in mine and yours. (I suppose I should copy yours and do the whole conversion to that, but it would be interesting to know what I'm missing.)

interesting

I think the reason is we want to make sure nf-core pipelines are backwards compatible to 23.04.0 for now. Sadly, it's just matching the string and not doing any clever semantic version checking. I've been disabling the CI checks recently (non nf-core pipelines) because they were changing too fast.

Those files are in tools, not in the pipelines it seems? This block in my

ci.yml

is maybe disabling the version test in some cases?

run: |
          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
          else
            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
          fi

It's part of

define_nxf_versions

which is referred to in my version of setting

NXF_VER

(see above). Still doesn't help me with linting, since changing to the #CE8SSJV3N version didn't help. (Sorry for my poor understanding of json.)

Those files are in tools, not in the pipelines it seems?

Correct, the linting error comes from tools

Right. Replacing the dynamic code I had with:

NXF_VER:
          - "23.04.0"
          - "latest-everything"

actually did the trick now that I tested again. Thanks. Is this because tools is somewhat behind and does a check that is a bit too hard-coded?

yup