Merge branch 'dev' into fix-files-unchanged-parital

nf-core · Feb 7, 2024 · 21c2c12 · 21c2c12
2 parents 9e219eb + 7899cd5
commit 21c2c12
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Showing 32 changed files with 103 additions and 86 deletions.
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -18,7 +18,7 @@ jobs:
       # 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@v2
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -17,7 +17,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -34,7 +34,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
 
@@ -63,7 +63,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"

diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # 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."

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -26,7 +26,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -42,12 +42,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: pip
@@ -59,7 +59,7 @@ jobs:
 
       # Set up Nextflow
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
         with:
           version: ${{ matrix.NXF_VER }}
 
@@ -147,7 +147,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-lint-wf/log.txt

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -39,7 +39,8 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
         runner:
-          - ${{ github.event.inputs.runners || 'self-hosted' }}
+          # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+          - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
         profile: ["self_hosted_runner"]
         include:
           - TEMPLATE: "template_skip_all.yml"
@@ -57,11 +58,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 
@@ -71,7 +72,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
         with:
           version: latest-everything
 
@@ -154,7 +155,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -26,7 +26,8 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -41,11 +42,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 
@@ -55,7 +56,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
         with:
           version: ${{ matrix.NXF_VER }}
 
@@ -68,7 +69,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,10 +18,10 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -72,7 +72,8 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # run on self-hosted runners for test_components.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ matrix.test == 'test_components.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails
@@ -83,11 +84,11 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -111,7 +112,7 @@ jobs:
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
 
       - name: Look if nf-test is already installed and write to env variable
         id: check-nftest
@@ -155,23 +156,24 @@ jobs:
           fi
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: coverage_${{ matrix.test }}
           path: .coverage
 
   coverage:
     needs: test
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     steps:
       - name: go to subdirectory
         run: |
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
@@ -188,14 +190,14 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@eaceaf801fd36c7dee90939fad912460b18a1ffe # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@f30e4959ba63075080d4f7f90cacc18d9f3fafd7 # v4
+      - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # v4
         with:
           files: coverage.xml
         env:

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -6,16 +6,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.x
           cache: pip
           cache-dependency-path: setup.py
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
 
       - name: Cache nf-test installation
         id: cache-software
@@ -36,7 +36,7 @@ jobs:
         run: pip install git+https://github.com/nf-core/tools.git@dev
 
       - name: Generate terminal images with rich-codex
-        uses: ewels/rich-codex@v1
+        uses: ewels/rich-codex@8ce988cc253c240a3027ba58e33e47640935dd8b # v1
         env:
           COLUMNS: 100
           HIDE_PROGRESS: "true"

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -23,7 +23,7 @@ concurrency:
 
 jobs:
   get-pipelines:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    runs-on: "ubuntu-latest"
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
@@ -38,15 +38,16 @@ jobs:
 
   sync:
     needs: get-pipelines
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     strategy:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -56,7 +57,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 
@@ -66,7 +67,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
         with:
           version: "latest-everything"
 
@@ -85,7 +86,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt