Merge pull request #2372 from mirpedrol/multiqc-cofig-links

Fix `multiqc_config.yml` links

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Template
 
+- Fix links in `multiqc_config.yml` ([#2372](https://github.com/nf-core/tools/pull/2372))
 - Remove default false from nextflow_schema.json ([#2376](https://github.com/nf-core/tools/pull/2376))
 - Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))
 

nf_core/bump_version.py

@@ -45,14 +45,19 @@ def bump_pipeline_version(pipeline_obj, new_version):
         ],
     )
     # multiqc_config.yaml
+    multiqc_new_version = "dev" if "dev" in new_version else new_version
     update_file_version(
         Path("assets", "multiqc_config.yml"),
         pipeline_obj,
         [
+            (
+                "/dev",
+                f"/{multiqc_new_version}",
+            ),
             (
                 rf"{re.escape(current_version)}",
-                f"{new_version}",
-            )
+                f"{multiqc_new_version}",
+            ),
         ],
     )
 

nf_core/lint/multiqc_config.py

@@ -72,12 +72,13 @@ def multiqc_config(self):
         # Check that the minimum plugins exist and are coming first in the summary
         try:
             version = self.nf_config.get("manifest.version", "").strip(" '\"")
+            version = "dev" if "dev" in version else version
             if "report_comment" not in mqc_yml:
                 raise AssertionError()
             if mqc_yml["report_comment"].strip() != (
-                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/{version}" '
+                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/tree/{version}" '
                 f'target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to '
-                f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/output" '
+                f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" '
                 'target="_blank">documentation</a>.'
             ):
                 raise AssertionError()

nf_core/pipeline-template/assets/multiqc_config.yml

@@ -1,7 +1,13 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/{{ name }}/{{ version}}" target="_blank">{{ name }}</a>
+  {% if 'dev' in version -%}
+  This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/{{ short_name }}/{{ version }}/output" target="_blank">documentation</a>.{% endif %}
+  <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
+  {%- else %}
+  This report has been generated by the <a href="https://github.com/{{ name }}/tree/{{ version }}" target="_blank">{{ name }}</a>
+  analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
+  {% endif %}
 report_section_order:
   "{{ name_noslash }}-methods-description":
     order: -1000