refactor example_worklfow test run into separate script to preserve a… #12
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test example.sh | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| # Cancel if a newer run is started | |
| # taken from https://github.com/nf-core/modules/blob/master/.github/workflows/nf-test.yml | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Build msyd | |
| uses: schneebergerlab/msyd@main | |
| with: | |
| python-version: "3.12" | |
| - name: Install other tools using conda | |
| run: | | |
| $CONDA/bin/conda install -c conda-forge -c bioconda "minimap2" | |
| - name: Test example_run.sh | |
| run: ./.github/workflows/run_test_example.sh |