Update data #42
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| name: Update data | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| on: | |
| pull_request: | |
| branches: main | |
| paths: | |
| - "data/**" | |
| - "scripts/**" | |
| - "workflow/**" | |
| - ".github/workflows/**" | |
| schedule: | |
| - cron: "45 2 1 * *" # Run monthly at 2:45 am | |
| workflow_dispatch: | |
| jobs: | |
| update: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Debug dump | |
| uses: crazy-max/ghaction-dump-context@v2 | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Miniconda environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| activate-environment: strchive | |
| environment-file: scripts/environment.yml | |
| python-version: 3.12 | |
| auto-activate-base: false | |
| - run: | | |
| conda info | |
| - name: Check loci and update bed files (short) | |
| if: ${{ github.event_name == 'pull_request'}} | |
| run: snakemake --config stages="skip-refs" | |
| # Enable this step to open an SSH session for debugging | |
| # - name: SSH debug | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Find new literature (intermediate) | |
| if: ${{ github.event_name == 'workflow_dispatch' }} | |
| run: | | |
| conda init | |
| source /home/runner/.bashrc | |
| conda activate strchive | |
| snakemake --config stages="new-refs" | |
| - name: Update all literature (long) | |
| if: ${{ github.event_name == 'schedule' }} | |
| run: | | |
| conda init | |
| source /home/runner/.bashrc | |
| conda activate strchive | |
| snakemake | |
| - name: Open pull request with updated files | |
| if: ${{ !(github.event_name == 'pull_request') }} | |
| uses: peter-evans/create-pull-request@v7 | |
| with: | |
| branch: update-data | |
| title: Update data | |
| - name: Commit updated files to current pull request | |
| if: ${{ github.event_name == 'pull_request' }} | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: Update data |