Add nextflow-lint pre-commit hook

[mashehu]

Supersedes #8391 (too many files changed in that PR) and #9726 (simpler setup)

[LouisLeNezet]

Shouldn't the pre-commit be ran only on the modified files ?
Currently it seems to run on all existing files.

The other issue, is that using the latest version of nextflow, generate new errors that I did not yet fix.
I think it would be best to use the stable release for this GA.

Similarly to what maxime did in his PR ?

      - name: Nextflow lint module ${{ matrix.module }}
        run: NXF_SYNTAX_PARSER=v2 nextflow lint modules/nf-core/${{ matrix.module }}

[mashehu]

Shouldn't the pre-commit be ran only on the modified files ?
Currently it seems to run on all existing files.

We had things slip through otherwise in the past. It is fast enough to run on all files, so this will keep the repo in better shape.

The other issue, is that using the latest version of nextflow, generate new errors that I did not yet fix.
I think it would be best to use the stable release for this GA.

I just wanted to test something, now back at latest stable (with the same error 🙁)

[LouisLeNezet]

The error is indeed strange as it does not appear locally.
However the incriminated modules does have an issue.
It should be

process {
    withName: COVERM_GENOME {
        ext.reference_mode = 'dir'   // force directory branch
        ext.args = '--genome-fasta-extension fasta'
    }
}

[LouisLeNezet]

It seems to be good now !

[LouisLeNezet]

Should we merge @mashehu ?