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Linting: Handle default values of type number from nextflow schema #2703

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merged 3 commits into from
Jan 30, 2024
Merged

Linting: Handle default values of type number from nextflow schema #2703

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23f0dae
handle default read as float when type is number
mirpedrol Jan 29, 2024
125d356
Merge branch 'dev' into linting-defaults
mirpedrol Jan 30, 2024
57e69a5
[automated] Update CHANGELOG.md
nf-core-bot Jan 30, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@

### Linting

- Handle default values of type number from nextflow schema ([#2703](https://github.com/nf-core/tools/pull/2703))

### Modules

### Subworkflows
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10 changes: 7 additions & 3 deletions nf_core/lint/nextflow_config.py
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Expand Up @@ -390,9 +390,13 @@ def nextflow_config(self):
if str(self.nf_config[param]) == schema_default:
passed.append(f"Config default value correct: {param}")
else:
failed.append(
f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
)
# Handle "number" type
if schema_default.endswith(".0") and str(self.nf_config[param]) == schema_default[:-2]:
passed.append(f"Config default value correct: {param}")
else:
failed.append(
f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
)
else:
failed.append(
f"Default value from the Nextflow schema '{param} = {self._wrap_quotes(schema_default)}' not found in `nextflow.config`."
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