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Lint the modules.json for uninstalled modules #1149

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Jul 5, 2021
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Co-authored-by: Erik Danielsson <53212377+ErikDanielsson@users.noreply.github.com>
KevinMenden and ErikDanielsson authored Jul 5, 2021

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commit d90d4de13d0c76b7c643150b540ceac45e290b49
2 changes: 1 addition & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -30,7 +30,7 @@
* Updated `nf-core modules remove` to remove module entry in `modules.json` if module directory is missing
* Create extra tempdir as work directory for `nf-core modules create-test-yml` to avoid adding the temporary files to the `test.yml`
* Refactored passing of command line arguments to `nf-core` commands and subcommands ([#1139](https://github.com/nf-core/tools/issues/1139), [#1140](https://github.com/nf-core/tools/issues/1140))
* Check for `modules.json` for entires of modules that are not actually installed in the pipeline [[#1141]](https://github.com/nf-core/tools/issues/1141)
* Check for `modules.json` for entries of modules that are not actually installed in the pipeline [[#1141](https://github.com/nf-core/tools/issues/1141)]

#### Sync

4 changes: 2 additions & 2 deletions nf_core/lint/modules_json.py
Original file line number Diff line number Diff line change
@@ -27,12 +27,12 @@ def modules_json(self):

for key in modules_json["modules"].keys():
if not key in module_remove.module_names:
failed.append(f"Entry for`{key}` found in `modules.json` but module is not installed in pipeline.")
failed.append(f"Entry for `{key}` found in `modules.json` but module is not installed in pipeline.")
all_modules_passed = False

if all_modules_passed:
passed.append("Only installed modules found in `modules.json`")
else:
warned.append("Could not open modules.json file.")
warned.append("Could not open `modules.json` file.")

return {"passed": passed, "warned": warned, "failed": failed}