From e3a5b70726a37c3f446c18e3245539cdeccdbab1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= <mashehu3@gmail.com>
Date: Fri, 11 Feb 2022 11:44:04 +0100
Subject: [PATCH 1/3] add github action for yamllint

---
 .github/workflows/yaml-lint.yml | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 .github/workflows/yaml-lint.yml

diff --git a/.github/workflows/yaml-lint.yml b/.github/workflows/yaml-lint.yml
new file mode 100644
index 0000000000..90d19f8259
--- /dev/null
+++ b/.github/workflows/yaml-lint.yml
@@ -0,0 +1,37 @@
+name: Lint YAML
+on: [push, pull_request]
+jobs:
+  YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v2
+      - name: Install yaml-lint
+        run: npm install -g yaml-lint
+      - name: Run yaml-lint
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.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" -o -name "*.yaml") -c ./.yamllint.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
\ No newline at end of file

From fad98f483d868d16bf6ce09d27367480696eac97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= <mashehu3@gmail.com>
Date: Fri, 11 Feb 2022 11:48:19 +0100
Subject: [PATCH 2/3] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0f494157b6..36bf00eb4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 * Add retry strategy for AWS megatests after releasing [nf-core/tower-action v2.2](https://github.com/nf-core/tower-action/releases/tag/v2.2)
 * Update igenomes path to the `BWAIndex` to fetch the whole `version0.6.0` folder instead of only the `genome.fa` file
 * Remove pinned Node version in the GitHub Actions workflows, to fix errors with `markdownlint`
+* Add yamllint GitHub Action.
 * Add `.yamllint.yml` to avoid line length and document start errors ([#1407](https://github.com/nf-core/tools/issues/1407))
 
 ## General

From fde544f0821bebdc55d57325e56cc485bbc672ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= <mashehu3@gmail.com>
Date: Fri, 11 Feb 2022 11:55:00 +0100
Subject: [PATCH 3/3] fix errors by newly introduced yaml-linting

---
 .github/workflows/push_dockerhub_dev.yml     | 1 -
 .github/workflows/tools-api-docs-release.yml | 6 +++---
 .github/workflows/yaml-lint.yml              | 2 +-
 .yamllint.yml                                | 3 ++-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index e0c26f2f4e..3a0e789d5b 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -27,4 +27,3 @@ jobs:
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push nfcore/tools:dev
-
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index 8c47f2dd0e..c420824722 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -9,9 +9,9 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        dir: 
-            - latest
-            - ${{ github.event.release.tag_name }}
+        dir:
+          - latest
+          - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v2
diff --git a/.github/workflows/yaml-lint.yml b/.github/workflows/yaml-lint.yml
index 90d19f8259..13a7aa23b4 100644
--- a/.github/workflows/yaml-lint.yml
+++ b/.github/workflows/yaml-lint.yml
@@ -34,4 +34,4 @@ jobs:
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
\ No newline at end of file
+          allow-repeats: false
diff --git a/.yamllint.yml b/.yamllint.yml
index 6889fa342e..e214bcc350 100644
--- a/.yamllint.yml
+++ b/.yamllint.yml
@@ -1,5 +1,6 @@
 extends: default
-
+ignore: |
+    nf_core/*-template/
 rules:
     document-start: disable
     line-length: disable