Merge pull request #1964 from mirpedrol/valid-dir

when pipeline dir doesn't contain `main.nf` or `nextflow.config`

CHANGELOG.md

@@ -20,6 +20,7 @@
 - Improve test coverage of sync.py
 - `check_up_to_date()` function from `modules_json` also checks for subworkflows.
 - The default branch can now be specified when creating a new pipeline repo [#1959](https://github.com/nf-core/tools/pull/1959).
+- Only warn when checking that the pipeline directory contains a `main.nf` and a `nextflow.config` file if the pipeline is not an nf-core pipeline [#1964](https://github.com/nf-core/tools/pull/1964)
 - Add file `versions.yml` when generating `test.yml` with `nf-core modules create-test-yml` but don't check for md5sum [#1963](https://github.com/nf-core/tools/pull/1963)
 
 ### Modules

nf_core/modules/modules_command.py

@@ -64,7 +64,9 @@ def has_valid_directory(self):
         main_nf = os.path.join(self.dir, "main.nf")
         nf_config = os.path.join(self.dir, "nextflow.config")
         if not os.path.exists(main_nf) and not os.path.exists(nf_config):
-            raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
+            if Path(self.dir).resolve().parts[-1].startswith("nf-core"):
+                raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
+            log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
         return True
 
     def has_modules_file(self):

tests/modules/install.py

@@ -22,7 +22,8 @@ def test_modules_install_nopipeline(self):
 @with_temporary_folder
 def test_modules_install_emptypipeline(self, tmpdir):
     """Test installing a module - empty dir given"""
-    self.mods_install.dir = tmpdir
+    os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
+    self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe")
     with pytest.raises(UserWarning) as excinfo:
         self.mods_install.install("foo")
     assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)