fix prev merge

.editorconfig

@@ -22,11 +22,3 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
-
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
-[*.{py}]
-indent_style = unset

.github/workflows/branch.yml

@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v2
+        uses: mshick/add-pr-comment@v1
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@v7
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/fix-linting.yml

@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  fix-linting:
+  deploy:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -13,77 +13,43 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
-      # indication that the linting is being fixed
-      - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: eyes
-
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
         run: gh pr checkout ${{ github.event.issue.number }}
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
-        with:
-          python-version: 3.11
+      - uses: actions/setup-node@v4
 
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
 
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
-        continue-on-error: true
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "result=pass" >> $GITHUB_OUTPUT
+          else
+            echo "result=fail" >> $GITHUB_OUTPUT
+          fi
 
-      # indication that the linting has finished
-      - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: "+1"
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
 
       - name: Commit & push changes
-        id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prettier_status.outputs.result == 'fail'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix code linting"
+          git commit -m "[automated] Fix linting with Prettier"
           git push
-
-      - name: react if linting errors were fixed
-        id: react-if-fixed
-        if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: hooray
-
-      - name: react if linting errors were not fixed
-        if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: confused
-
-      - name: react if linting errors were not fixed
-        if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          issue-number: ${{ github.event.issue.number }}
-          body: |
-            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/genomic-medicine-sweden/tomte/actions/runs/${{ github.run_id }}) for more details.

.github/workflows/linting.yml

@@ -11,22 +11,61 @@ on:
     types: [published]
 
 jobs:
-  pre-commit:
+  EditorConfig:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      - uses: actions/setup-node@v4
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile\|.bed\|.tsv')
+
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-node@v4
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
+
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # 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:
-          python-version: 3.11
-          cache: "pip"
+          message: |
+            ## Python linting (`black`) 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 [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
 
-      - name: Install pre-commit
-        run: pip install pre-commit
+            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!
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
 
   nf-core:
     runs-on: ubuntu-latest
@@ -37,7 +76,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -60,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@v2
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@v0.1.0
+      - uses: zentered/bluesky-post-action@v0.0.2
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

.gitpod.yml

@@ -7,7 +7,6 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
-
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

.pre-commit-config.yaml

@@ -1,10 +1,5 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v2.7.1"
     hooks:
       - id: prettier
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
-    hooks:
-      - id: editorconfig-checker
-        alias: ec

assets/email_template.html

@@ -12,7 +12,7 @@
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>genomic-medicine-sweden/tomte ${version}</h1>
+<h1>genomic-medicine-sweden/tomte v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){

lib/WorkflowMain.groovy

@@ -24,7 +24,7 @@ class WorkflowMain {
     //
     // Validate parameters and print summary to screen
     //
-    public static void initialise(workflow, params, log, args) {
+    public static void initialise(workflow, params, log) {
 
         // Print workflow version and exit on --version
         if (params.version) {
@@ -35,8 +35,6 @@ class WorkflowMain {
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
-        // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
-        checkProfile(workflow.profile, args, log)
 
         // Check that conda channels are set-up correctly
         if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -62,16 +60,4 @@ class WorkflowMain {
         }
         return null
     }
-
-    //
-    // Exit pipeline if --profile contains spaces
-    //
-    private static void checkProfile(profile, args, log) {
-        if (profile.endsWith(',')) {
-            Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
-        }
-        if (args[0]) {
-            log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n      Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
-        }
-    }
 }

main.nf

@@ -61,7 +61,7 @@ if (params.validate_params) {
     validateParameters()
 }
 
-WorkflowMain.initialise(workflow, params, log, args)
+WorkflowMain.initialise(workflow, params, log)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~