Merge branch 'dev' into nf-core-template-merge-3.2.0

Author: muffato

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,6 +2,14 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [sanger-tol/blobtoolkit pipeline documentation](https://pipelines.tol.sanger.ac.uk/blobtoolkit/usage)
+
   - type: textarea
     id: description
     attributes:

.github/workflows/ci.yml

@@ -21,26 +21,24 @@ concurrency:
 jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
+    # Only run on push if this is the dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/blobtoolkit') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        # "conda" is not supported
         profile:
-          - "conda"
           - "docker"
           - "singularity"
         test_name:
           - "test"
         isMaster:
-          - ${{ github.base_ref == 'master' }}
+          - ${{ github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
         exclude:
-          - isMaster: false
-            profile: "conda"
           - isMaster: false
             profile: "singularity"
     steps:

.github/workflows/fix-linting.yml

@@ -8,14 +8,14 @@ jobs:
     # 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/') &&
-      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      contains(github.event.comment.body, '@sanger-tolsoft fix linting') &&
       github.repository == 'sanger-tol/blobtoolkit'
     runs-on: ubuntu-latest
     steps:
-      # Use the @nf-core-bot token to check out so we can push later
+      # Use the @sanger-tolsoft token to check out so we can push later
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
-          token: ${{ secrets.nf_core_bot_auth_token }}
+          token: ${{ secrets.sangertolsoft_access_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
@@ -29,7 +29,7 @@ jobs:
       - name: Checkout Pull Request
         run: gh pr checkout ${{ github.event.issue.number }}
         env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+          GITHUB_TOKEN: ${{ secrets.sangertolsoft_access_token }}
 
       # Install and run pre-commit
       - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
@@ -56,8 +56,8 @@ jobs:
         id: commit-and-push
         if: steps.pre-commit.outcome == 'failure'
         run: |
-          git config user.email "core@nf-co.re"
-          git config user.name "nf-core-bot"
+          git config user.email "105875386+sanger-tolsoft@users.noreply.github.com"
+          git config user.name "sanger-tolsoft"
           git config push.default upstream
           git add .
           git status

.github/workflows/sanger_test.yml

@@ -0,0 +1,34 @@
+name: sanger-tol LSF tests
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Sets env vars for workflow_dispatch
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'workflow_dispatch'
+
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV_LARGE }}
+          revision: ${{ env.REVISION }}
+          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
+          parameters: |
+            {
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
+              "use_work_dir_as_temp": true,
+            }
+          profiles: test,sanger,singularity,cleanup
+      - uses: actions/upload-artifact@v4
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/sanger_test_full.yml

@@ -0,0 +1,42 @@
+name: sanger-tol LSF full size tests
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF full size tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Sets env vars for push
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'push'
+
+      - name: Sets env vars for workflow_dispatch
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'workflow_dispatch'
+
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ env.REVISION }}
+          workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
+          parameters: |
+            {
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
+            }
+          profiles: test_full,sanger,singularity,cleanup
+      - uses: actions/upload-artifact@v4
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json