A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Having an issue with subworkflow `bam_create_som_pon_gatk`, that is not valid with pre-commit on the pipeline side, but ok from the modules side

we should probably add `modules/nf-core` and `subworkflows/nf-core` to `.prettierignore`

with pre-commit:
```prettier.................................................................Failed
- hook id: prettier
- files were modified by this hook

modules/nf-core/gatk4/mutect2/meta.yml
subworkflows/nf-core/bam_create_som_pon_gatk/meta.yml```
After a TEMPLATE sync and a subworkflows update

why do we have this then in the pre-commit yaml?
```      - id: end-of-file-fixer
        exclude: |
          (?x)^(
              .*ro-crate-metadata.json$|
              modules/nf-core/.*|
              subworkflows/nf-core/.*|
              .*\.snap$
          )$```

and I do believe code coming from modules should be pre-commit valid

they have the same prettier version in `pre-commit-config.yml`?

the `end-of-file-fixer` is just a replacement for what we had in editorconfig

```diff .pre-commit-config.yaml ../modules/.pre-commit-config.yaml
7a8
&gt; 
9c10
&lt;     rev: v6.0.0
---
&gt;     rev: v5.0.0```
PR incoming

Any smart idea on how to have a proper sync between TEMPLATE in pipelines and modules?

Anyhow this is for my issue: <https://github.com/nf-core/modules/pull/9313>

yes: <https://github.com/nf-core/tools/pull/3858> :wink:

I was more thinking of having a TEMPLATE merge on modules

for that, we should first split up the renovate PRs into infra and module containers

this is not an issue of modules template. more of the modules repo itself

Actually given that modules in the pipeline could be old, that is an ok solution for me

it does make sense to ignore linting, but for me, new code coming from modules should always be valid no matter what

try running `pre-commit run --all-files` in modules...

and since we are not properly in sync for the template in pipelines and modules, that's why I was thinking towards more of a template issue (not module, but pipeline given the pre-commit.yaml files etc)

That'll be for another PR, but yeah, we should do this more often

<https://github.com/nf-core/modules/pull/9314>