switch tests to build in conda env #23
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| 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 minimap2 manually # conda doesn't seem to work | |
| # run: | | |
| # curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf - | |
| # mv minimap2-2.28_x64-linux\/minimap2 ./ | |
| # ./minimap2 -h # test it worked & is callable | |
| - name: Test example_run.sh | |
| run: ./.github/workflows/run_test_example.sh | |
| shell: bash |