From debf9b7d139b60afccbe0a901eb0b910db284ed3 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 24 Oct 2024 16:26:48 +0000
Subject: [PATCH] Update GitHub Actions

---
 .github/workflows/changelog.yml                        |  6 +++---
 .github/workflows/create-lint-wf.yml                   |  4 ++--
 .github/workflows/create-test-lint-wf-template.yml     |  6 +++---
 .github/workflows/create-test-wf.yml                   |  4 ++--
 .github/workflows/deploy-pypi.yml                      |  4 ++--
 .github/workflows/fix-linting.yml                      |  4 ++--
 .github/workflows/lint-code.yml                        |  4 ++--
 .github/workflows/push_dockerhub_dev.yml               |  2 +-
 .github/workflows/push_dockerhub_release.yml           |  2 +-
 .github/workflows/pytest.yml                           | 10 +++++-----
 .github/workflows/sync.yml                             |  6 +++---
 .github/workflows/update-textual-snapshots.yml         |  4 ++--
 .github/workflows/update_components_template.yml       |  4 ++--
 nf_core/pipeline-template/.github/workflows/ci.yml     |  2 +-
 .../.github/workflows/download_pipeline.yml            |  2 +-
 .../.github/workflows/fix-linting.yml                  |  4 ++--
 .../pipeline-template/.github/workflows/linting.yml    |  8 ++++----
 .../.github/workflows/release-announcements.yml        |  2 +-
 .../.github/workflows/template_version_comment.yml     |  2 +-
 19 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index e89f6ff87..d4fe34c25 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 5e32c4280..37ab71bc3 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -48,12 +48,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: pip
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 627b73fb6..2672d1e21 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -40,7 +40,7 @@ jobs:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
       - name: checkout
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -77,11 +77,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index a6f3b5ac6..93581b915 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -48,11 +48,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 0e7ddf675..d2b631f15 100644
--- 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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 9feff8d51..6d749b0d9 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 9581fa18b..7ffd6e9df 100644
--- 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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 3d676eabd..6409335ac 100644
--- 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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 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
index 4b7e8aacb..d29b03b68 100644
--- 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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 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
index 2f48e67b5..90bf384b7 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -61,7 +61,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -87,11 +87,11 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -172,9 +172,9 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 42d0f5c09..625f00d24 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -60,10 +60,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -73,7 +73,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index 32983d38c..9706ef55c 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -33,7 +33,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"
diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml
index 86e6ba7b8..575065d38 100644
--- a/.github/workflows/update_components_template.yml
+++ b/.github/workflows/update_components_template.yml
@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.x"
 
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 33631fdc5..9db393d9f 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 6ba251e52..56208537c 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -35,7 +35,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 13992f5c5..4fa3d54d7 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 878998ad9..cfdbcc12a 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
index a200d141e..e1b654d34 100644
--- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml
+++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml
index 51f2f7f94..27737afb4 100644
--- a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}