From 62efc60c1c319b08a656fb7b0c62fd0d5d4d8e51 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 24 Nov 2025 11:33:13 +0000 Subject: [PATCH] Update actions/checkout action to v6 --- .github/workflows/changelog.yml | 2 +- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/deploy-pypi.yml | 2 +- .github/workflows/fix-linting.yml | 2 +- .github/workflows/lint-code.yml | 2 +- .github/workflows/nextflow-source-test.yml | 4 ++-- .github/workflows/push_dockerhub_dev.yml | 2 +- .github/workflows/push_dockerhub_release.yml | 2 +- .github/workflows/pytest.yml | 6 +++--- .github/workflows/sync.yml | 4 ++-- .github/workflows/test_offline_configs.yml | 4 ++-- .github/workflows/update-template-snapshots.yml | 4 ++-- .github/workflows/update-textual-snapshots.yml | 2 +- nf_core/pipeline-template/.github/workflows/fix_linting.yml | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 4 ++-- nf_core/pipeline-template/.github/workflows/nf-test.yml | 4 ++-- .../.github/workflows/template-version-comment.yml | 2 +- 19 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 682a834b4c..777b48d984 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -19,7 +19,7 @@ jobs: ) steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index fa7a0f6ae7..77b93fa788 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -42,7 +42,7 @@ jobs: export NXF_WORK=$(pwd) # Get the repo code - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out source-code repository # Set up nf-core/tools diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index f70ed7014f..b8aea533bb 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -32,7 +32,7 @@ jobs: all_features: ${{ steps.create_matrix.outputs.matrix }} steps: - name: checkout - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Create Matrix id: create_matrix run: | @@ -56,7 +56,7 @@ jobs: steps: - name: Check out source-code repository - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 91b80c3657..b5d15aa447 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -41,7 +41,7 @@ jobs: cd create-test-wf export NXF_WORK=$(pwd) - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out source-code repository - name: Set up Python 3.14 diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index c1a392f45b..12e4dcaeb2 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out source-code repository - name: Set up Python 3.14 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 3fd67bf0a9..dfe609cd2d 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index ea771554e0..954b85a127 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -20,7 +20,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml index 0b1614ab31..28bbab1f6d 100644 --- a/.github/workflows/nextflow-source-test.yml +++ b/.github/workflows/nextflow-source-test.yml @@ -14,12 +14,12 @@ jobs: steps: - name: Check out Nextflow - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: repository: nextflow-io/nextflow path: nextflow - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out nf-core/tools with: ref: dev diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index 9224eabbde..0bcaf4e3c8 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -22,7 +22,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up QEMU for multi-architecture build uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3 diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml index 7121eea6af..e6688644d2 100644 --- a/.github/workflows/push_dockerhub_release.yml +++ b/.github/workflows/push_dockerhub_release.yml @@ -22,7 +22,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up QEMU for multi-architecture build uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3 diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 5b6c429b80..2c5795a3ce 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -35,7 +35,7 @@ jobs: name: Get test file matrix runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out source-code repository - name: List tests @@ -64,7 +64,7 @@ jobs: cd pytest export NXF_WORK=$(pwd) - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out source-code repository - name: Set up Python ${{ matrix.python-version }} @@ -138,7 +138,7 @@ jobs: - runs-on=${{ github.run_id }}-coverage - runner=2cpu-linux-x64 steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index 99b379a11d..2149879bf2 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -62,12 +62,12 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out nf-core/tools with: ref: ${{ github.ref_name }} - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} diff --git a/.github/workflows/test_offline_configs.yml b/.github/workflows/test_offline_configs.yml index ebf9c3d6bd..6eaa08778f 100644 --- a/.github/workflows/test_offline_configs.yml +++ b/.github/workflows/test_offline_configs.yml @@ -53,11 +53,11 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out nf-core/tools with: ref: ${{ github.ref_name }} - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index 37fd771641..0aaacfcda2 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -17,7 +17,7 @@ jobs: all_features: ${{ steps.create_matrix.outputs.matrix }} steps: - name: checkout - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Create Matrix id: create_matrix @@ -36,7 +36,7 @@ jobs: fail-fast: false steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index 015da3ef2c..9d87503e02 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml index eb91004e21..9aa0a2e0bd 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 1dd75aaad8..8bc500551a 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -11,7 +11,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index e83129aa84..5c9f85afcd 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -41,7 +41,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: fetch-depth: 0 @@ -87,7 +87,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: fetch-depth: 0 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 46e59e5cad..f2ede5d4a3 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6 with: ref: ${{ github.event.pull_request.head.sha }}