corrected spelling mistake #12
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| name: cdiff food bourne infection workflow | |
| on: | |
| push: | |
| branches: ["main"] | |
| tags-ignore: | |
| - "**" | |
| pull_request: | |
| branches: ["main"] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| # step 1: checkout repository | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| # step 2 use environment.yml dependencies to create conda environment | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: cdiff_pipeline | |
| python-version: ${{ matrix.python-version }} | |
| # step 3 | |
| - name: Install custom tool | |
| run: | | |
| git clone https://github.com/ssi-dk/serum_readfilter | |
| cd serum_readfilter | |
| pip install . | |
| cd .. | |
| # step 4 | |
| #- name: Run test script | |
| # run: | | |
| # conda activate cdiff_pipeline | |
| # make test | |
| # step 5 | |
| - name: Check git tag and create a new tag if tests pass | |
| if: ${{ success() }} | |
| run: | | |
| COMMIT_SHORT=$(git rev-parse --short=7 HEAD) | |
| DIR_NAME=$(basename $(pwd)) | |
| TAG_NAME="${DIR_NAME}.${GITHUB_SHA::7}.$(date +%d-%m-%Y)" | |
| git tag $TAG_NAME | |
| git push origin $TAG_NAME --no-verify | |
| echo "$TAG_NAME" | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Step 6: Trigger bifrost_sp_cdiff workflow | |
| - name: Workflow dispatch with API - trigger bifrost_sp_cdiff workflow | |
| if: ${{ success() }} | |
| run: | | |
| curl -v -L \ | |
| -X POST \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "Authorization: Bearer ${{ secrets.FBI_DISPATCH_TOKEN }}" \ | |
| https://api.github.com/repos/ssi-dk/bifrost_sp_cdiff/dispatches \ | |
| -d '{"event_type":"cdiff-fbi-webhook"}' |