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run pre-comit when rendering template for pipelines sync #3371

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merged 6 commits into from
Jan 13, 2025
Merged

run pre-comit when rendering template for pipelines sync #3371

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20de879
fix trailing spaces in conf/test.config
mirpedrol Dec 20, 2024
3cb8775
run pre-comit when rendering template for pipelines sync
mirpedrol Dec 20, 2024
6b43881
add newline
mirpedrol Dec 20, 2024
4bd4d23
bump to 3.1.2dev
mirpedrol Dec 20, 2024
9cc2b5b
Merge branch 'dev' into run-prettier-on-sync
mirpedrol Jan 13, 2025
80e06dc
do not run pre-commit if we are not on a git repo
mirpedrol Jan 13, 2025
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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/conf/test.config
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Expand Up @@ -27,7 +27,7 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'

{% if igenomes -%}
{%- if igenomes -%}
// Genome references
genome = 'R64-1-1'
{%- endif %}
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3 changes: 3 additions & 0 deletions nf_core/pipelines/create/create.py
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Expand Up @@ -386,6 +386,9 @@ def render_template(self) -> None:
yaml.dump(config_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper())
log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")

# Run prettier on files for pipelines sync
run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])

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Needs more testing 👀

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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

def fix_linting(self):
"""
Updates the .nf-core.yml with linting configurations
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