Important! Template update for nf-core/tools v2.12

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python and markdown (is taken care off by prettier)
+[*.{py,md}]
+indent_style = unset

.github/CONTRIBUTING.md

@@ -53,9 +53,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
-- Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+-   On your own fork, make a new branch `patch` based on `upstream/master`.
+-   Fix the bug, and bump version (X.Y.Z+1).
+-   A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
@@ -96,8 +96,8 @@ The process resources can be passed on to the tool dynamically within the proces
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-- initial process channel: `ch_output_from_<process>`
-- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+-   initial process channel: `ch_output_from_<process>`
+-   intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 
@@ -113,11 +113,11 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/sarek/codespaces)
-- Tools installed
-  - nf-core
-  - Nextflow
+-   Open the repo in [Codespaces](https://github.com/nf-core/sarek/codespaces)
+-   Tools installed
+    -   nf-core
+    -   Nextflow
 
 Devcontainer specs:
 
-- [DevContainer config](.devcontainer/devcontainer.json)
+-   [DevContainer config](.devcontainer/devcontainer.json)

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,14 +13,14 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
 
 ## PR checklist
 
-- [ ] This comment contains a description of changes (with reason).
-- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
-- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
-- [ ] Usage Documentation in `docs/usage.md` is updated.
-- [ ] Output Documentation in `docs/output.md` is updated.
-- [ ] `CHANGELOG.md` is updated.
-- [ ] `README.md` is updated (including new tool citations and authors/contributors).
+-   [ ] This comment contains a description of changes (with reason).
+-   [ ] If you've fixed a bug or added code that should be tested, add tests!
+-   [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
+-   [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+-   [ ] Make sure your code lints (`nf-core lint`).
+-   [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+-   [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+-   [ ] Usage Documentation in `docs/usage.md` is updated.
+-   [ ] Output Documentation in `docs/output.md` is updated.
+-   [ ] `CHANGELOG.md` is updated.
+-   [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/RELEASE_CHECKLIST.md

@@ -3,16 +3,22 @@
 > This checklist is for our own reference, to help us prepare a new release
 
 1. Check that everything is ready to go
-   - Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
-   - [GHA CI](https://github.com/nf-core/sarek/actions/workflows/ci.yml) are passing on `dev`
-   - [GHA linting](https://github.com/nf-core/sarek/actions/workflows/linting.yml) are passing on `dev`
+
+-   Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
+-   [GHA CI](https://github.com/nf-core/sarek/actions/workflows/ci.yml) are passing on `dev`
+-   [GHA linting](https://github.com/nf-core/sarek/actions/workflows/linting.yml) are passing on `dev`
+
 2. Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html)
 3. Choose an appropriate codename for the release (if major or minor)
-   - i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
+
+-   i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
+
 4. Sync `dev` and checkout a new branch for the release
 5. Bump version:
-   - `nf-core bump-version . <VERSION>`
-   - edit `CHANGELOG`
+
+-   `nf-core bump-version . <VERSION>`
+-   edit `CHANGELOG`
+
 6. Make a PR to `master`
 7. Wait for reviews
 8. Merge said PR
@@ -21,15 +27,19 @@
 11. RT the nf-core automated tweet about the new released version
 12. Make a new branch from `dev`
 13. Checkout the `CHANGELOG.md` from `master`
-    - `git checkout upstream/master -- CHANGELOG.md`
+
+-   `git checkout upstream/master -- CHANGELOG.md`
+
 14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
 15. Checkout figures from `master`
-    - `git checkout upstream/master -- docs/images/sarek_indices_subway.svg`
-    - `git checkout upstream/master -- docs/images/sarek_indices_subway.png`
-    - `git checkout upstream/master -- docs/images/sarek_subway.svg`
-    - `git checkout upstream/master -- docs/images/sarek_subway.png`
-    - `git checkout upstream/master -- docs/images/sarek_workflow.svg`
-    - `git checkout upstream/master -- docs/images/sarek_workflow.png`
+
+-   `git checkout upstream/master -- docs/images/sarek_indices_subway.svg`
+-   `git checkout upstream/master -- docs/images/sarek_indices_subway.png`
+-   `git checkout upstream/master -- docs/images/sarek_subway.svg`
+-   `git checkout upstream/master -- docs/images/sarek_subway.png`
+-   `git checkout upstream/master -- docs/images/sarek_workflow.svg`
+-   `git checkout upstream/master -- docs/images/sarek_workflow.png`
+
 16. Make a PR to `dev`
 17. Wait for review
 18. Merge said PR

.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@v1
+        uses: mshick/add-pr-comment@v2
         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@v7
+      - uses: actions/stale@v9
         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/download_pipeline.yml

@@ -0,0 +1,67 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to master branch
+#  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://github.com/nf-core/tools.git@dev
+
+      - name: Get the repository name and current branch set as environment variable
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+
+      - name: Download the pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+        run: |
+          nf-core download  ${{ env.REPO_LOWERCASE }} \
+          --revision ${{ env.REPO_BRANCH }} \
+          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          --compress "none" \
+          --container-system 'singularity' \
+          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-cache-utilisation 'amend' \
+          --download-configuration
+
+      - name: Inspect download
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+
+      - name: Run the downloaded pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

.github/workflows/fix-linting.yml

@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # 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/') &&
@@ -13,43 +13,77 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # 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 }}
 
-      - uses: actions/setup-node@v4
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # 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
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      # 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: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           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/nf-core/sarek/actions/runs/${{ github.run_id }}) for more details.