Merge pull request #2254 from mashehu/lint-for-zenodo-doi

remove bioconda badge check comment, add zenodo doi check

.github/workflows/create-lint-wf.yml

@@ -84,6 +84,10 @@ jobs:
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
 
+      # Replace zenodo.XXXXXX to pass readme linting
+      - name: replace zenodo.XXXXXX
+        run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned

CHANGELOG.md

@@ -16,12 +16,14 @@
 - Simplify pipeline README ([#2186](https://github.com/nf-core/tools/issues/2186))
 - Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133]
 - Add tower.yml file to the pipeline template ([#2251](https://github.com/nf-core/tools/pull/2251))
+- Add mastodon badge to README ([#2253](https://github.com/nf-core/tools/pull/2253))
 
 ### Linting
 
 - Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
 - Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
 - `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+- Warn if `/zenodo.XXXXXX` is present in the Readme ([#2254](https://github.com/nf-core/tools/pull/2254))
 
 ### Modules
 

nf_core/lint/readme.py

@@ -17,16 +17,12 @@ def readme(self):
 
            [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
 
-    * Bioconda badge
+    .. note:: This badge are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
 
-      * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required
-      * Required badge code:
+    * Zenodo release
 
-        .. code-block:: md
-
-           [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
+        * If pipeline is released but still contains a 'zenodo.XXXXXXX' tag, the test fails
 
-    .. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
     """
     passed = []
     warned = []
@@ -62,4 +58,16 @@ def readme(self):
         else:
             warned.append("README did not have a Nextflow minimum version badge.")
 
+    if "zenodo_doi" not in ignore_configs:
+        # Check that zenodo.XXXXXXX has been replaced with the zendo.DOI
+        zenodo_re = r"/zenodo\.X+"
+        match = re.search(zenodo_re, content)
+        if match:
+            warned.append(
+                "README contains the placeholder `zenodo.XXXXXXX`. "
+                "This should be replaced with the zenodo doi (after the first release)."
+            )
+        else:
+            passed.append("README Zenodo placeholder was replaced with DOI.")
+
     return {"passed": passed, "warned": warned, "failed": failed}