Is it expected that a cross-organisational subworkflow should fail linting? Have I missed something in the YAML formatting?

The meta.yml of the subworkflow hic_mapping is not valid:

{'minimap2/index': {'git_remote': '<https://github.com/nf-core/modules.git'}}> is not of type 'string'. Check the entry for components.

meta.yml file looks like the following:

components:
  - hiccramalign/chunks
  - hiccramalign/bwamem2align
  - hiccramalign/minimap2align
  - samtools/index:
      git_remote: <https://github.com/nf-core/modules.git>
  - samtools/faidx:
      git_remote: <https://github.com/nf-core/modules.git>
  - samtools/merge:
      git_remote: <https://github.com/nf-core/modules.git>
  - samtools/markdup:
      git_remote: <https://github.com/nf-core/modules.git>
  - bwamem2/index:
      git_remote: <https://github.com/nf-core/modules.git>
  - minimap2/index:
      git_remote: <https://github.com/nf-core/modules.git>

Not sure if linting is supported for these but one thing that might be worth checking is whether your custom remote has the updated

meta.yml

schema to match the nf-core remote (required to allow the new cross-repo support)

It does look like it's correct, I think https://github.com/sanger-tol/nf-core-modules/blob/main/subworkflows/yaml-schema.json

Oh heh it's the one in the nf-core remote which doesn't allow

object

so my guess is that your lint command is using that one for whatever reason

It's happening in two places - locally and on a GitHub runner -so might be a tools bug?

Maybe. I suspect that the issue is you are running lint on these subworkflows but not pointing at the right yaml-schema. Whether that's a tools bug or you need to adjust your lint command I am not sure.

I don't see an option in the lint command to specify a schema. Do you know if the schema is referenced somewhere in a config file in the repository?

It shouldn't be. The main thing is that for linting cross-repo subworkflows you will need to make sure your lint command has the right

-g

and other remote options (in this case I would have expected it to error before this if it didn't though so maybe there is a bug)

Oh, linting with

-g

fixes the issue (and reveals fun new issues)

That one may well be a bug in the way it gets the components from the meta.yml but you'll need to look at the command code to find that out probably