Merge pull request nf-core#3005 from nvnieuwk/add-org-to-tag

Add organization to `main.nf.test` tag instead of using `nfcore`

CHANGELOG.md

@@ -14,6 +14,8 @@
 
 ### Components
 
+- The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
+
 ### General
 
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))

nf_core/components/create.py

@@ -157,6 +157,10 @@ def create(self):
             if self.component_type == "modules":
                 self._get_module_structure_components()
 
+        # Add a valid organization name for nf-test tags
+        not_alphabet = re.compile(r"[^a-zA-Z]")
+        self.org_alphabet = not_alphabet.sub("", self.org)
+
         # Create component template with jinja2
         self._render_template()
         log.info(f"Created component template: '{self.component_name}'")

nf_core/module-template/tests/main.nf.test.j2

@@ -7,7 +7,7 @@ nextflow_process {
     process "{{ component_name_underscore|upper }}"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_{{ org_alphabet }}"
     {%- if subtool %}
     tag "{{ component }}"
     {%- endif %}

nf_core/modules/lint/module_tests.py

@@ -4,6 +4,7 @@
 
 import json
 import logging
+import re
 from pathlib import Path
 
 import yaml
@@ -137,7 +138,10 @@ def module_tests(_, module: NFCoreComponent):
                     )
             # Verify that tags are correct.
             main_nf_tags = module._get_main_nf_tags(module.nftest_main_nf)
-            required_tags = ["modules", "modules_nfcore", module.component_name]
+            not_alphabet = re.compile(r"[^a-zA-Z]")
+            org_alp = not_alphabet.sub("", module.org)
+            org_alphabet = org_alp if org_alp != "" else "nfcore"
+            required_tags = ["modules", f"modules_{org_alphabet}", module.component_name]
             if module.component_name.count("/") == 1:
                 required_tags.append(module.component_name.split("/")[0])
             chained_components_tags = module._get_included_components_in_chained_tests(module.nftest_main_nf)

nf_core/subworkflow-template/tests/main.nf.test.j2

@@ -7,7 +7,7 @@ nextflow_workflow {
     workflow "{{ component_name_underscore|upper }}"
 
     tag "subworkflows"
-    tag "subworkflows_nfcore"
+    tag "subworkflows_{{ org_alphabet }}"
     tag "subworkflows/{{ component_name }}"
     // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
     tag "samtools"

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -4,6 +4,7 @@
 
 import json
 import logging
+import re
 from pathlib import Path
 
 import yaml
@@ -144,10 +145,13 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                     )
             # Verify that tags are correct.
             main_nf_tags = subworkflow._get_main_nf_tags(subworkflow.nftest_main_nf)
+            not_alphabet = re.compile(r"[^a-zA-Z]")
+            org_alp = not_alphabet.sub("", subworkflow.org)
+            org_alphabet = org_alp if org_alp != "" else "nfcore"
             required_tags = [
                 "subworkflows",
                 f"subworkflows/{subworkflow.component_name}",
-                "subworkflows_nfcore",
+                f"subworkflows_{org_alphabet}",
             ]
             included_components = []
             if subworkflow.main_nf.is_file():