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6 changes: 3 additions & 3 deletions .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,14 @@ jobs:
python-version: ["3.11"]

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v7
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
uses: actions/setup-python@v7
with:
python-version: ${{ matrix.python-version }}
cache: "pip"
- name: Install nextflow
uses: nf-core/setup-nextflow@v2
uses: nf-core/setup-nextflow@v3
with:
version: "24.04.4"
- name: Install dependencies
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/docker.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,8 @@ jobs:
if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: pietrobolcato/action-read-yaml@1.0.0
- uses: actions/checkout@v7
- uses: pietrobolcato/action-read-yaml@1.1.0
id: metadata
with:
config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
Expand All @@ -39,12 +39,12 @@ jobs:
echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
- name: Login to DockerHub
#if: github.event_name != 'pull_request'
uses: docker/login-action@v2
uses: docker/login-action@v4
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build and push
uses: docker/build-push-action@v4
uses: docker/build-push-action@v7
# only try building & pushing the container if parsing the metadata worked
if: ${{ steps.metadata.outputs['container'] != '' }}
with:
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/docs-mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@ jobs:
mkdocs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v7
with:
fetch-depth: 0
- uses: CCBR/actions/mkdocs-mike@v0.2
- uses: CCBR/actions/mkdocs-mike@v0.7
with:
github-token: ${{ github.token }}
4 changes: 2 additions & 2 deletions .github/workflows/draft-release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,10 @@ jobs:
draft-release:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v7
with:
fetch-depth: 0 # required to include tags
- uses: CCBR/actions/draft-release@v0.2
- uses: CCBR/actions/draft-release@v0.7
with:
github-token: ${{ github.token }}
version-tag: ${{ github.event.inputs.version-tag }}
4 changes: 2 additions & 2 deletions .github/workflows/post-release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@ jobs:
cleanup:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v7
with:
fetch-depth: 0
- uses: CCBR/actions/post-release@v0.2
- uses: CCBR/actions/post-release@v0.7
with:
github-token: ${{ github.token }}
4 changes: 2 additions & 2 deletions .github/workflows/techdev-project.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,13 @@ jobs:
- name: Generate a token
id: generate-token
if: ${{ inputs.github-token == '' }}
uses: actions/create-github-app-token@v2
uses: actions/create-github-app-token@v3
with:
app-id: ${{ vars.CCBR_BOT_APP_ID }}
private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
owner: CCBR

- uses: actions/add-to-project@v1.0.2
- uses: actions/add-to-project@v2.0.0
with:
project-url: https://github.com/orgs/CCBR/projects/17
github-token: ${{ steps.generate-token.outputs.token }}
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