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Dump template yml to file in pipeline repo after creation #2189

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merged 6 commits into from
Mar 27, 2023
Merged

Dump template yml to file in pipeline repo after creation #2189

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6d68f11
Dump template yml to file in pipeline repo after creation
awgymer Feb 22, 2023
834c0ec
Make the dump conditional on template yaml having content
awgymer Feb 22, 2023
d88756b
Add test for pipeline init with template yml
awgymer Mar 27, 2023
87020c5
Merge branch 'dev' into template-yml-to-file-on-create
awgymer Mar 27, 2023
637e967
Add test mocking cli input
awgymer Mar 27, 2023
326e600
Add check to ensure output yml matches expected
awgymer Mar 27, 2023
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9 changes: 7 additions & 2 deletions nf_core/create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ def __init__(
plain=False,
default_branch=None,
):
self.template_params, skip_paths_keys = self.create_param_dict(
self.template_params, skip_paths_keys, self.template_yaml = self.create_param_dict(
name, description, author, version, template_yaml_path, plain
)

Expand Down Expand Up @@ -178,7 +178,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
if not re.match(r"^[a-z]+$", param_dict["short_name"]):
raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")

return param_dict, skip_paths
return param_dict, skip_paths, template_yaml

def customize_template(self, template_areas):
"""Customizes the template parameters.
Expand Down Expand Up @@ -348,6 +348,11 @@ def render_template(self):
# Update the .nf-core.yml with linting configurations
self.fix_linting()

log.debug("Dumping pipeline template yml to file")
if self.template_yaml:
with open(self.outdir / "pipeline_template.yml", "w") as fh:
yaml.safe_dump(self.template_yaml, fh)
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Suggested change
yaml.safe_dump(self.template_yaml, fh)
yaml.safe_dump(self.template_yaml, fh)
run_prettier_on_file(fh.name)

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So this should only trigger when a template_yml is either supplied (which perhaps is silly) or someone customises something on the CLI.

Currently there are no tests which mock passing information in via the CLI prompts that I'm aware of. Happy to try adding them but not sure if it's best done as a unit-test or as part of one of the fuller tests defined in the GH actions?


def update_nextflow_schema(self):
"""
Removes unused parameters from the nextflow schema.
Expand Down