Merge pull request #3034 from mashehu/prettier-dbl-quotes

switch prettier config to double quotes

.github/ISSUE_TEMPLATE/config.yml

@@ -3,6 +3,6 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: 'Slack #website channel'
+  - name: "Slack #website channel"
     url: https://nfcore.slack.com/channels/website
     about: Discussion about the nf-core website

.github/rich-codex.yml

@@ -62,7 +62,7 @@ outputs:
     img_paths:
       - public/images/tools/nf-core-list-stars.svg
   - command: nf-core pipelines launch rnaseq -r 3.8.1
-    trim_after: 'Command line'
+    trim_after: "Command line"
     img_paths:
       - public/images/tools/nf-core-launch-rnaseq.svg
   - command: mkdir tmp && cd tmp && nf-core pipelines download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d
@@ -173,7 +173,7 @@ outputs:
   - command: cd tmp/modules && nf-core modules test fastqc --no-prompts
     timeout: 30
     extra_env:
-      PROFILE: 'conda'
+      PROFILE: "conda"
     fake_command: nf-core modules test fastqc --no-prompts
     img_paths:
       - public/images/tools/nf-core-modules-test.svg
@@ -233,13 +233,13 @@ outputs:
   - command: cd tmp/modules && nf-core subworkflows test bam_rseqc --no-prompts
     timeout: 30
     extra_env:
-      PROFILE: 'conda'
+      PROFILE: "conda"
     fake_command: nf-core subworkflows test bam_rseqc --no-prompts
     img_paths:
       - public/images/tools/nf-core-subworkflows-test.svg
   - command: cd tmp/modules && nf-core subworkflows lint bam_stats_samtools
     extra_env:
-      PROFILE: 'conda'
+      PROFILE: "conda"
     fake_command: nf-core subworkflows lint bam_stats_samtools
     img_paths:
       - public/images/tools/nf-core-subworkflows-lint.svg

.github/workflows/add-netlify-link.yml

@@ -3,8 +3,8 @@ name: Add Netlify Link to PR
 on:
   pull_request_target:
     paths:
-      - 'sites/**/src/pages/**'
-      - 'sites/**/src/content/**'
+      - "sites/**/src/pages/**"
+      - "sites/**/src/content/**"
 
 jobs:
   add-comment:

.github/workflows/add-tools-api-docs.yml

@@ -3,9 +3,9 @@ on:
   workflow_dispatch:
     inputs:
       ref_name:
-        description: 'The name of the release branch'
+        description: "The name of the release branch"
         required: true
-        default: 'dev'
+        default: "dev"
 
 jobs:
   api-docs:
@@ -16,14 +16,14 @@ jobs:
       - name: Checkout tools code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
-          repository: 'nf-core/tools'
+          repository: "nf-core/tools"
           ref: ${{ inputs.ref_name }}
-          path: 'tools'
+          path: "tools"
 
       - name: setup node
         uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
         with:
-          node-version: '20'
+          node-version: "20"
 
       - name: Install dependencies
         run: |
@@ -80,7 +80,7 @@ jobs:
           body: |
             This PR updates the nf-core/tools API docs for ${{inputs.ref_name}}.
             Please review the changes and merge if they look good.
-          branch: 'update-api-docs-${{inputs.ref_name}}'
+          branch: "update-api-docs-${{inputs.ref_name}}"
           delete-branch: true
-          base: 'main'
+          base: "main"
           draft: false

.github/workflows/blueskyfeedbot.yml

@@ -2,7 +2,7 @@ name: Bluesky FeedBot
 on:
   schedule:
     # This will run every hour
-    - cron: '0 * * * *'
+    - cron: "0 * * * *"
   workflow_dispatch:
 jobs:
   rss-to-bluesky:
@@ -21,7 +21,7 @@ jobs:
           key: feed-cache-${{ steps.generate-key.outputs.cache-key }}
           restore-keys: feed-cache-
       - name: GitHub
-        uses: 'joschi/[email protected]'
+        uses: "joschi/[email protected]"
         with:
           # This is the RSS feed you want to publish
           rss-feed: https://nf-co.re/blog/rss.xml
@@ -32,7 +32,7 @@ jobs:
           # This is your service URL (optional)
           service-url: https://bsky.social
           # This is the Bluesky username (example: username.bsky.social)
-          username: 'nf-co.re'
+          username: "nf-co.re"
           # This is the app password you created earlier
           password: ${{ secrets.FEED_TO_BLUESKY }}
           # This is a path to the cache file, using the above cache path

.github/workflows/broken-link-checker.yml

@@ -2,7 +2,7 @@ name: Check Broken Links
 
 on:
   schedule:
-    - cron: '0 0 * * *' # This will run daily at 00:00
+    - cron: "0 0 * * *" # This will run daily at 00:00
 
 jobs:
   linkChecker:
@@ -12,10 +12,10 @@ jobs:
         uses: jakepartusch/wait-for-netlify-action@f1e137043864b9ab9034ae3a5adc1c108e3f1a48 # v1.4
         id: waitFor200
         with:
-          site_name: 'nf-core'
+          site_name: "nf-core"
           max_timeout: 600 # 10 Minutes
       - name: Check for broken links
         uses: JustinBeckwith/linkinator-action@3d5ba091319fa7b0ac14703761eebb7d100e6f6d # v1
         with:
-          paths: 'https://deploy-preview-${{github.event.pull_request.number}}--nf-core.netlify.app'
+          paths: "https://deploy-preview-${{github.event.pull_request.number}}--nf-core.netlify.app"
           recurse: true

.github/workflows/build-json-files-and-md-cache.yml

@@ -2,7 +2,7 @@ name: build json files and md-cache
 
 on:
   schedule: # every day at 2am and 2pm
-    - cron: '0 2,14 * * *'
+    - cron: "0 2,14 * * *"
   workflow_dispatch:
   repository_dispatch:
     types: [update-website]
@@ -25,7 +25,7 @@ jobs:
         uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
         with:
           node-version: 20
-          cache: 'npm'
+          cache: "npm"
 
       - name: Install dependencies
         run: npm ci
@@ -90,9 +90,9 @@ jobs:
         uses: peter-evans/create-pull-request@67ccf781d68cd99b580ae25a5c18a1cc84ffff1f # v7
         with:
           token: ${{ secrets.CREATE_PR_TOKEN }}
-          commit-message: 'chore: update pipeline.json and component.json'
-          title: 'chore: update pipeline.json and component.json'
-          body: 'This PR was automatically created by a GitHub Action because there were too many lines changed in the pipeline.json and component.json files.'
-          branch: 'chore/update-pipeline-json-and-component-json'
+          commit-message: "chore: update pipeline.json and component.json"
+          title: "chore: update pipeline.json and component.json"
+          body: "This PR was automatically created by a GitHub Action because there were too many lines changed in the pipeline.json and component.json files."
+          branch: "chore/update-pipeline-json-and-component-json"
           delete-branch: true
           draft: false

.github/workflows/fix-linting.yml

@@ -56,7 +56,7 @@ jobs:
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: '+1'
+          reactions: "+1"
 
       - name: Commit & push changes
         id: commit-and-push

.github/workflows/playwright.yml

@@ -2,7 +2,7 @@ name: Playwright Tests
 on:
   pull_request:
     paths:
-      - 'sites/**'
+      - "sites/**"
 
 # Cancel if a newer run is started
 concurrency:
@@ -18,7 +18,7 @@ jobs:
       - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
         with:
           node-version: 18
-          cache: 'npm'
+          cache: "npm"
       - name: Install dependencies
         run: npm ci
       - name: Install Playwright Browsers
@@ -27,7 +27,7 @@ jobs:
         uses: jakepartusch/wait-for-netlify-action@f1e137043864b9ab9034ae3a5adc1c108e3f1a48 # v1.4
         id: waitFor200
         with:
-          site_name: 'nf-core-main-site'
+          site_name: "nf-core-main-site"
           max_timeout: 180 # 3 Minutes
       - name: determine the changed directory
         id: determine_changed_directory
@@ -40,7 +40,7 @@ jobs:
             npm run test -w sites/main-site
           # done
         env:
-          PLAYWRIGHT_TEST_BASE_URL: 'https://deploy-preview-${{github.event.pull_request.number}}--nf-core-main-site.netlify.app'
+          PLAYWRIGHT_TEST_BASE_URL: "https://deploy-preview-${{github.event.pull_request.number}}--nf-core-main-site.netlify.app"
       - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
         if: always()
         with:

.github/workflows/rich-codex.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: "20"
 
       - name: Set up Python
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
@@ -42,13 +42,13 @@ jobs:
         uses: ewels/rich-codex@8ce988cc253c240a3027ba58e33e47640935dd8b # v1
         env:
           COLUMNS: 100
-          HIDE_PROGRESS: 'true'
+          HIDE_PROGRESS: "true"
           NXF_ANSI_LOG: false
         with:
-          commit_changes: 'true'
+          commit_changes: "true"
           terminal_width: 100
-          skip_git_checks: 'true'
-          search_include: '.github/workflows/rich-codex.yml'
+          skip_git_checks: "true"
+          search_include: ".github/workflows/rich-codex.yml"
 
       - name: Restore package.json
         run: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: 'v3.1.0'
+    rev: "v3.1.0"
     hooks:
       - id: prettier
         # NOTE https://github.com/pre-commit/pre-commit/issues/3133

.prettierrc.cjs

@@ -1,10 +1,5 @@
 module.exports = {
-    // TODO: REMOVE SINGLE QUOTES CONFIG LATER
-    // Leaving it for now to minimise diffs, but double quote is more consistent with the rest of nf-core
-    singleQuote: true,
     trailingComma: 'all',
-    //////
-
     printWidth: 120,
 
     plugins: ['prettier-plugin-astro', 'prettier-plugin-svelte'],

README.md

@@ -124,7 +124,7 @@ You can show a short announcement banner on the website by adding additional inf
 
 ```yaml
 announcement:
-  text: 'Your announcement text'
+  text: "Your announcement text"
   start: YYYY-MM-DDTHH:MM:SS+HH:MM # Start date and time of the announcement (without quotes!)
   end: YYYY-MM-DDTHH:MM:SS+HH:MM # End date and time of the announcement. (without quotes!) This is an optional field for events, where the start date of the event is the end date of the announcement by default.
 ```