Merge pull request #3826 from mirpedrol/update-template-modules

update pipeline template subworkflows

Author: mirpedrol

CHANGELOG.md

@@ -15,6 +15,7 @@
 - Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756))
 - Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781))
 - update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788))
+- update pipeline template subworkflows ([#3826](https://github.com/nf-core/tools/pull/3826))
 - fix AWS tests launch action ([#3827](https://github.com/nf-core/tools/pull/3827))
 
 ### Linting

nf_core/pipeline-template/modules.json

@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {

nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml

@@ -98,12 +98,12 @@ def test_list_files_no_git(self, tmpdir):
         files = pipeline_obj.list_files()
         assert tmp_fn in files
 
-    @mock.patch("os.path.exists")
-    @mock.patch("os.makedirs")
-    def test_request_cant_create_cache(self, mock_mkd, mock_exists):
+    @mock.patch("pathlib.Path.mkdir")
+    @mock.patch("pathlib.Path.exists")
+    def test_request_cant_create_cache(self, mock_exists, mock_mkdir):
         """Test that we don't get an error when we can't create cachedirs"""
-        mock_mkd.side_effect = PermissionError()
         mock_exists.return_value = False
+        mock_mkdir.side_effect = PermissionError()
         nf_core.utils.setup_requests_cachedir()
 
     def test_pip_package_pass(self):