Merge pull request #3767 from rrahn/feature/dynamic-org-for-linting

SZhengP · web-flow · commit 4164503749d2 · 2025-09-24T13:21:01.000-04:00
Use the org from the .nf-core.yml when linting manifest name and homePage.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@
 
 - ignore files in gitignore also for pipeline_if_empty_null lint test ([#3722](https://github.com/nf-core/tools/pull/3722))
 - do not check pytest_modules.yml file, deprecating ([#3748](https://github.com/nf-core/tools/pull/3748))
+- Use the org from the .nf-core.yml when linting manifest name and homePage. ([#3767](https://github.com/nf-core/tools/pull/3767))
 
 ### Modules
 
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
@@ -5,6 +5,7 @@
 from typing import Optional, Union
 
 from nf_core.pipelines.schema import PipelineSchema
+from nf_core.utils import load_tools_config
 
 log = logging.getLogger(__name__)
 
@@ -255,30 +256,35 @@ def nextflow_config(self) -> dict[str, list[str]]:
         else:
             failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``")
 
+    _, nf_core_yaml_config = load_tools_config(self.wf_path)
+    org_name = "nf-core"
+    if nf_core_yaml_config and getattr(nf_core_yaml_config, "template", None):
+        org_name = getattr(nf_core_yaml_config.template, "org", org_name) or org_name
+
     if "manifest.name" not in ignore_configs:
         # Check that the pipeline name starts with nf-core
         try:
             manifest_name = self.nf_config.get("manifest.name", "").strip("'\"")
-            if not manifest_name.startswith("nf-core/"):
+            if not manifest_name.startswith(f"{org_name}/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
-            failed.append(f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}")
+            failed.append(f"Config ``manifest.name`` did not begin with ``{org_name}/``:\n    {manifest_name}")
         else:
-            passed.append("Config ``manifest.name`` began with ``nf-core/``")
+            passed.append(f"Config ``manifest.name`` began with ``{org_name}/``")
 
     if "manifest.homePage" not in ignore_configs:
         # Check that the homePage is set to the GitHub URL
         try:
             manifest_homepage = self.nf_config.get("manifest.homePage", "").strip("'\"")
-            if not manifest_homepage.startswith("https://github.com/nf-core/"):
+            if not manifest_homepage.startswith(f"https://github.com/{org_name}/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
             failed.append(
-                f"Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {manifest_homepage}"
+                f"Config variable ``manifest.homePage`` did not begin with https://github.com/{org_name}/:\n    {manifest_homepage}"
             )
 
         else:
-            passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
+            passed.append(f"Config variable ``manifest.homePage`` began with https://github.com/{org_name}/")
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
