run pre-comit when rendering template for pipelines sync #3371
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mashehu
approved these changes
Dec 20, 2024
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mirpedrol
commented
Dec 20, 2024
nf_core/pipelines/create/create.py
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| # Run prettier on files for pipelines sync | ||
| run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")]) | ||
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Tested, it runs prettier, it doesn't fix editorconfig errors, but the error found in test.config is fixed by this PR. I have also added a check to only run pre-commit if we are on a git repo, that way we won't run prettier when creating a pipeline as the repo is not initialised yet
mashehu
approved these changes
Jan 13, 2025
| @@ -70,6 +70,15 @@ def print_fixes(lint_obj): | |||
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| def check_git_repo() -> bool: | |||
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I thought we had already a function like this, but doesn't look like it.
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Pre-commit was not running when creating a pipeline (because there isn't a git repo yet at the point of creating the pipeline), but it is running when we use
nf-core pipelines syncand create a new pipeline in theTEMPLATEbranchShould fix #3372