Merge pull request #460 from apeltzer/singularity-lint

Check for singularity file and raise error if found

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 * Updated Blacklist of synced pipelines
 * Ignore pre-releases in `nf-core list`
+* Lint for `Singularity` file [and remove it](https://github.com/nf-core/tools/issues/458)
 
 ### Linting
 

docs/lint_errors.md

@@ -227,3 +227,7 @@ The nf-core workflow template contains a number of comment lines with the follow
 ```
 
 This lint test runs through all files in the pipeline and searches for these lines.
+
+## Error #11 - Singularity file found ##{#11}
+
+As we are relying on [Docker Hub](https://https://hub.docker.com/) instead of Singularity and all containers are automatically pulled from there, repositories should not have a `Singularity` file present.

nf_core/lint.py

@@ -166,6 +166,7 @@ def lint_pipeline(self, release_mode=False):
             'check_files_exist',
             'check_licence',
             'check_docker',
+            'check_singularity',
             'check_nextflow_config',
             'check_ci_config',
             'check_readme',
@@ -277,6 +278,12 @@ def check_docker(self):
 
         self.failed.append((2, "Dockerfile check failed"))
 
+    def check_singularity(self):
+        """Checks whether a Singularity file exists and warns to remove that file then."""
+        fn = os.path.join(self.path, "Singularity")
+        if(os.path.exists(fn)):
+            self.failed.append((11, "Singularity file exists"))
+
     def check_licence(self):
         """Checks licence file is MIT.
 

tests/lint_examples/failing_example/Singularity

@@ -0,0 +1 @@
+Nothing to be found here

tests/test_lint.py

@@ -107,6 +107,13 @@ def test_mit_license_example_with_failed(self):
         bad_lint_obj.check_licence()
         expectations = {"failed": 1, "warned": 0, "passed": 0}
         self.assess_lint_status(bad_lint_obj, **expectations)
+
+    def test_singularity_with_failed(self):
+        """Tests that Singularity file doesn't exist"""
+        bad_lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
+        bad_lint_obj.check_singularity()
+        expectations = {"failed": 1, "warned": 0, "passed": 0}
+        self.assess_lint_status(bad_lint_obj, **expectations)
 
     def test_config_variable_example_pass(self):
         """Tests that config variable existence test works with good pipeline example"""