nf-core · ewels · Mar 23, 2021 · Mar 23, 2021 · Mar 23, 2021 · Mar 23, 2021
diff --git a/.github/workflows/markdown-lint.yml b/.github/workflows/markdown-lint.yml
@@ -30,13 +30,14 @@ jobs:
 
             * Install `markdownlint-cli`
                 * On Mac: `brew install markdownlint-cli`
-                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli): `npm install -g markdownlint-cli`
-            * Try to automatically fix errors in your pipeline: `markdownlint . --config .github/markdownlint.yml --fix`
-            * Check that there are no remaining problems: `markdownlint . --config .github/markdownlint.yml`
+                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
+            * Fix the markdown errors
+                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
+                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,7 +6,7 @@
 * Fixed parameter validation bug caused by JSONObject [[#937](https://github.com/nf-core/tools/issues/937)]
 * Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
 * Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
-* Added automated PR comments to the Markdownlint and Python Black lint CI tests to explain failures
+* Added automated PR comments to the Markdown, YAML and Python lint CI tests to explain failures (tools and pipeline template)
 
 ## [v1.13.1 - Copper Crocodile Patch :crocodile: :pirate_flag:](https://github.com/nf-core/tools/releases/tag/1.13.1) - [2021-03-19]
 

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -1,4 +1,4 @@
-name: nf-core linting
+{% raw %}name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
 on:
@@ -19,6 +19,34 @@ jobs:
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Markdown linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `markdownlint-cli`
+                * On Mac: `brew install markdownlint-cli`
+                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
+            * Fix the markdown errors
+                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
+                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   YAML:
     runs-on: ubuntu-latest
     steps:
@@ -30,6 +58,33 @@ jobs:
         run: npm install -g yaml-lint
       - name: Run yaml-lint
         run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## YAML linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `yaml-lint`
+                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Fix the markdown errors
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml")`
+                * Fix any reported errors in your YAML files
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
@@ -53,7 +108,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install nf-core
-{% raw %}
+
       - name: Run nf-core lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}