Merge branch 'dev' into initial-git-branch-setting

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Fix lint warnings for `samplesheet_check.nf` module
+- Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
 
 ### Linting
 

nf_core/create.py

@@ -167,6 +167,11 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
  param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
  param_dict["version"] = version
 
+ # Check that the pipeline name matches the requirements
+ if not re.match(r"^[a-z]+$", param_dict["short_name"]):
+ log.error("[red]Invalid workflow name: must be lowercase without punctuation.")
+ sys.exit(1)
+
  return param_dict, skip_paths
 
  def customize_template(self, template_areas):

tests/test_launch.py

@@ -73,7 +73,7 @@ def test_make_pipeline_schema(self, tmp_path):
  """Create a workflow, but delete the schema file, then try to load it"""
  test_pipeline_dir = os.path.join(tmp_path, "wf")
  create_obj = nf_core.create.PipelineCreate(
- "test_pipeline", "", "", outdir=test_pipeline_dir, no_git=True, plain=True
+ "testpipeline", "", "", outdir=test_pipeline_dir, no_git=True, plain=True
  )
  create_obj.init_pipeline()
  os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json"))

tests/test_schema.py

@@ -31,7 +31,7 @@ def setUp(self):
  self.tmp_dir = tempfile.mkdtemp()
  self.template_dir = os.path.join(self.tmp_dir, "wf")
  create_obj = nf_core.create.PipelineCreate(
- "test_pipeline", "", "", outdir=self.template_dir, no_git=True, plain=True
+ "testpipeline", "", "", outdir=self.template_dir, no_git=True, plain=True
  )
  create_obj.init_pipeline()
 

tests/test_sync.py

@@ -25,7 +25,7 @@ class TestModules(unittest.TestCase):
  def setUp(self):
  """Create a new pipeline to test"""
  self.tmp_dir = tempfile.mkdtemp()
- self.pipeline_dir = os.path.join(self.tmp_dir, "test_pipeline")
+ self.pipeline_dir = os.path.join(self.tmp_dir, "testpipeline")
  default_branch = "master"
  self.create_obj = nf_core.create.PipelineCreate(
  "testing", "test pipeline", "tester", outdir=self.pipeline_dir, plain=True, default_branch=default_branch