nf-core · SZhengP · Oct 6, 2025 · Oct 4, 2025 · Oct 4, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@
 - 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))
+- Use the org from .nf-core.yml when linting multiqc_config report_comment ([#3800](https://github.com/nf-core/tools/pull/3800))
 
 ### Modules
 

diff --git a/nf_core/pipelines/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py
@@ -3,6 +3,7 @@
 import yaml
 
 from nf_core.pipelines.lint_utils import ignore_file
+from nf_core.utils import load_tools_config
 
 
 def multiqc_config(self) -> dict[str, list[str]]:
@@ -98,17 +99,24 @@ def multiqc_config(self) -> dict[str, list[str]]:
         if "report_comment" not in ignore_configs:
             # Check that the minimum plugins exist and are coming first in the summary
             version = self.nf_config.get("manifest.version", "").strip(" '\"")
+
+            # Get the org from .nf-core.yml config, defaulting to "nf-core"
+            _, 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 "dev" in version:
                 version = "dev"
                 report_comments = (
-                    f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/tree/dev" target="_blank">nf-core/{self.pipeline_name}</a>'
+                    f'This report has been generated by the <a href="https://github.com/{org_name}/{self.pipeline_name}/tree/dev" target="_blank">{org_name}/{self.pipeline_name}</a>'
                     f" analysis pipeline. For information about how to interpret these results, please see the "
                     f'<a href="https://nf-co.re/{self.pipeline_name}/dev/docs/output" target="_blank">documentation</a>.'
                 )
 
             else:
                 report_comments = (
-                    f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/releases/tag/{version}" target="_blank">nf-core/{self.pipeline_name}</a>'
+                    f'This report has been generated by the <a href="https://github.com/{org_name}/{self.pipeline_name}/releases/tag/{version}" target="_blank">{org_name}/{self.pipeline_name}</a>'
                     f" analysis pipeline. For information about how to interpret these results, please see the "
                     f'<a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" target="_blank">documentation</a>.'
                 )