nf-core · mashehu · Feb 6, 2024 · Feb 6, 2024
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
@@ -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
@@ -57,11 +57,11 @@ 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 +71,7 @@ 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 +154,7 @@ 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
@@ -41,11 +41,11 @@ 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 +55,7 @@ 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 +68,7 @@ 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
@@ -83,11 +83,11 @@ 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: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -111,7 +111,7 @@ jobs:
         run: echo "date=$(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
@@ -155,7 +155,7 @@ jobs:
           fi
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: coverage_${{ matrix.test }}
           path: .coverage
@@ -169,9 +169,9 @@ jobs:
           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:
@@ -188,7 +188,7 @@ 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*

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
@@ -43,10 +43,10 @@ jobs:
       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 +56,7 @@ 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 +66,7 @@ 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 +85,7 @@ 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
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
@@ -24,10 +24,10 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        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
 
@@ -43,7 +43,7 @@ jobs:
       - name: Sync dev docs
         # Only sync with the website if it was a push from nf-core/tools dev branch
         if: github.repository == 'nf-core/tools' && github.event_name == 'push' && github.event.ref == 'refs/heads/dev'
-        uses: SamKirkland/FTP-Deploy-Action@v4.3.4
+        uses: SamKirkland/FTP-Deploy-Action@8a24039354ee91000cb948cb4a1dbdf1a1b94a3c # v4.3.4
         with:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}

diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
@@ -19,10 +19,10 @@ jobs:
           - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
-        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
 
@@ -37,7 +37,7 @@ jobs:
 
       - name: Sync release docs
         if: github.repository == 'nf-core/tools'
-        uses: SamKirkland/FTP-Deploy-Action@v4.3.4
+        uses: SamKirkland/FTP-Deploy-Action@8a24039354ee91000cb948cb4a1dbdf1a1b94a3c # v4.3.4
         with:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11-slim
+FROM python:3.11-slim@sha256:53d6284a40eae6b625f22870f5faba6c54f2a28db9027408f4dee111f1e885a2
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for the nfcore tools"
 

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,7 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
-FROM gitpod/workspace-base
+FROM gitpod/workspace-base@sha256:7a130ed80741c3f838a7607f88296d26ac477e713c12b638ab93874d3169f7f1
 
 USER root
 

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters {%- raw %}
@@ -31,7 +31,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: Tower debug log file
           path: |