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

nf-core

Hi everyone !
On the <https://nf-co.re/pipeline_health> checks we have many pipeline with the `master` as default branch.
Do we have a simple way to change the default branch for all the pipelines or should each maintainer do it manually and what would be the best procedure ?

i would say each maintainer does it for theirs <https://nf-co.re/docs/tutorials/pipelines/switching_master_to_main>

It seems I don't have the permission for phaseimpute eventhough I'm the maintainer.
Can anyone give me the rights to do it ?

When I try : `nf-core pipelines sync` I'm getting
```/PROGS/conda/llenezet/envs/env_nf/lib/python3.14/site-packages/click/core.py:1223: UserWarning: The parameter -b is used more than once. Remove its duplicate as parameters should be unique.
  parser = self.make_parser(ctx)
/PROGS/conda/llenezet/envs/env_nf/lib/python3.14/site-packages/click/core.py:1216: UserWarning: The parameter -b is used more than once. Remove its duplicate as parameters should be unique.
  self.parse_args(ctx, args)
WARNING  Could not find GitHub authentication token. Some API requests may fail.                                                                               
INFO     Pipeline directory: /WORKING_DIRECTORY/llenezet/phaseimpute                                                                                           
INFO     Original pipeline repository branch is 'dev'                                                                                                          
INFO     Deleting tracked files in 'TEMPLATE' branch                                                                                                           
INFO     Making a new template pipeline using pipeline variables                                                                                               
INFO     Saving metadata file to '/WORKING_DIRECTORY/llenezet/phaseimpute'                                                                                     
ERROR    Failed to rebuild pipeline from template with error:                                                                                                  
         [Errno 7] Argument list too long: 'pre-commit'```

I guess this is due to `pipeline_create_obj.init_pipeline()` that calls `run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])` through `render_template()` .
We might want to change it to run it on all files for that.

Here is the PR to fix it !
<https://github.com/nf-core/tools/pull/4097>

For posterity information:
After debugging with a local version of nf-core the issue was the presence of the .nf-test/ folder inducing lots of changes.
Removing it solved the issue.

Aaah, no after deleting `.nf-test` and any other dir `work`, `null`, `testing`, ... the issue still persists with me.

Kinda a cryptic error message but renaming the default branch from `master` to `main` solved the  `[Errno 7] Argument list too long: prek`  error for me when running `nf-core pipelines sync`