Merge pull request #1568 from ewels/fix-1562

Make module template and `test_yml_builder` default commands match.

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
 - Add `.prettierignore` file to stop Prettier linting tests from running over test files
 - Add actions workflow to respond to `@nf-core-bot fix linting` comments on pipeline PRs
+- Made module template test command match the default used in `nf-core modules create-test-yml` ([#1562](https://github.com/nf-core/tools/issues/1562))
 
 ### General
 

nf_core/modules/test_yml_builder.py

@@ -164,9 +164,9 @@ def build_single_test(self, entry_point):
                 ep_test["name"] = rich.prompt.Prompt.ask("[violet]Test name", default=default_val).strip()
 
         while ep_test["command"] == "":
-            default_val = (
-                f"nextflow run tests/modules/{self.module_name} -entry {entry_point} -c tests/config/nextflow.config"
-            )
+            # Don't think we need the last `-c` flag, but keeping to avoid having to update 100s modules.
+            # See https://github.com/nf-core/tools/issues/1562
+            default_val = f"nextflow run ./tests/modules/{self.module_name} -entry {entry_point} -c ./tests/config/nextflow.config  -c ./tests/modules/{self.module_name}/nextflow.config"
             if self.no_prompts:
                 ep_test["command"] = default_val
             else: