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Add pipeline verification function to nf-core lint #1208

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merged 3 commits into from
Jul 16, 2021
Merged

Add pipeline verification function to nf-core lint #1208

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e6f8519
Add pipelint validation function to 'nf-core lint'
ErikDanielsson Jul 16, 2021
eedfb7a
Update CHANGELOG.md
ErikDanielsson Jul 16, 2021
f60d25b
Merge branch 'dev' of https://github.com/nf-core/tools into modules-j…
ErikDanielsson Jul 16, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@
### Modules

* Added consistency checks between installed modules and `modules.json` ([#1199](https://github.com/nf-core/tools/issues/1199))
* Added missing function call to `nf-core lint` ([#1198](https://github.com/nf-core/tools/issues/1198))
* Fix `nf-core lint` not filtering modules test when run with `--key` ([#1203](https://github.com/nf-core/tools/issues/1203))

## [v2.0.1 - Palladium Platypus Junior](https://github.com/nf-core/tools/releases/tag/2.0.1) - [2021-07-13]
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6 changes: 6 additions & 0 deletions nf_core/lint/__init__.py
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Expand Up @@ -68,6 +68,12 @@ def run_linting(
# Create the modules lint object
module_lint_obj = ModuleLint(pipeline_dir)

# Verify that the pipeline is correctly configured
try:
module_lint_obj.has_valid_directory()
except UserWarning:
raise

# Run only the tests we want
if key:
# Select only the module lint tests
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