diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 5318d2a0c4..cebcc854bc 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -19,7 +19,7 @@ jobs: ) steps: - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 521f5d038f..03b9aa2411 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -48,7 +48,7 @@ jobs: export NXF_WORK=$(pwd) # Get the repo code - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 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 1634ade745..0de7287a57 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -61,7 +61,7 @@ jobs: cd create-lint-wf-template export NXF_WORK=$(pwd) - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out source-code repository - name: Set up Python 3.12 diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index d752e26713..87cdf2e7bb 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -48,7 +48,7 @@ jobs: cd create-test-wf export NXF_WORK=$(pwd) - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out source-code repository - name: Set up Python 3.12 diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index 0afe47b751..1202891e4d 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out source-code repository - name: Set up Python 3.12 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index b89dd44aa9..4334871c4c 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 9a9eb31bc0..3bddd42d49 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -18,7 +18,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python 3.12 uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index 360c863af6..c613e13a2d 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Build nfcore/tools:dev docker image run: docker build --no-cache . -t nfcore/tools:dev diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml index 1babf607d7..5a076f6d3b 100644 --- a/.github/workflows/push_dockerhub_release.yml +++ b/.github/workflows/push_dockerhub_release.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Build nfcore/tools:latest docker image run: docker build --no-cache . -t nfcore/tools:latest diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 0d51739bf9..03576fa310 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -61,7 +61,7 @@ jobs: name: Get test file matrix runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out source-code repository - name: List tests @@ -87,7 +87,7 @@ jobs: cd pytest export NXF_WORK=$(pwd) - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out source-code repository - name: Set up Python ${{ needs.setup.outputs.python-version }} @@ -158,7 +158,7 @@ jobs: mkdir -p pytest cd pytest - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python 3.12 uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 env: @@ -177,7 +177,7 @@ jobs: mv .github/.coveragerc . - name: Download all artifacts - uses: actions/download-artifact@9c19ed7fe5d278cd354c7dfd5d3b88589c7e2395 # v4 + uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 - name: Run coverage run: | coverage combine --keep coverage*/.coverage* diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml index 016f20ab0e..cd12b139d3 100644 --- a/.github/workflows/rich-codex.yml +++ b/.github/workflows/rich-codex.yml @@ -6,7 +6,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repo - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index 43bab50bbf..15802cdef2 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -44,10 +44,10 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out nf-core/tools - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml index d3690af6e3..5ba513735e 100644 --- a/.github/workflows/update_components_template.yml +++ b/.github/workflows/update_components_template.yml @@ -11,7 +11,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 diff --git a/CHANGELOG.md b/CHANGELOG.md index 08ef6ed61e..b618f947ba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -60,6 +60,7 @@ - Update GitHub Actions ([#2927](https://github.com/nf-core/tools/pull/2927)) - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933)) +- Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index 9603a597a9..6b2547765d 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -28,7 +28,7 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml index 1dc4be0113..18e6f9e158 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 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 2e75daf1a9..d1ecae12b7 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -14,7 +14,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Set up Python 3.12 uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 @@ -32,7 +32,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2