Merge pull request #1208 from ErikDanielsson/modules-json-creation-lint

Add pipeline verification function to `nf-core lint`
nf-core · Jul 16, 2021 · 5342803 · 5342803
2 parents 2d32038 + f60d25b
commit 5342803
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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]

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
@@ -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