addapt pytest according to not skipping github

nf-core · Jun 20, 2023 · fd34e7a · fd34e7a
1 parent 3936854
commit fd34e7a
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/nf_core/create.py b/nf_core/create.py
@@ -352,6 +352,7 @@ def render_template(self):
         if self.template_yaml:
             with open(self.outdir / "pipeline_template.yml", "w") as fh:
                 yaml.safe_dump(self.template_yaml, fh)
+            run_prettier_on_file(self.outdir / "pipeline_template.yml")
 
     def update_nextflow_schema(self):
         """

diff --git a/tests/test_create.py b/tests/test_create.py
@@ -124,7 +124,7 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
-        assert not os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
 
         # Check pipeline yml has been dumped and matches input
         pipeline_template = os.path.join(pipeline.outdir, "pipeline_template.yml")
@@ -134,5 +134,5 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
 
         # Check that some of the skipped files are not present
         assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md"))
-        assert not os.path.exists(os.path.join(pipeline.outdir, ".github"))
+        assert not os.path.exists(os.path.join(pipeline.outdir, ".github", "workflows"))
         assert not os.path.exists(os.path.join(pipeline.outdir, "conf", "igenomes.config"))