add conda dep install to integrated test #9
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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 other tools using conda | |
| run: | | |
| $CONDA/bin/conda install -c conda-forge -c bioconda "minimap2" | |
| - name: Test example_run.sh | |
| run: | | |
| # alias to a call launching the syri entrypoint from python | |
| # necessary, as the hacky git install does not install the CLI entrypoints | |
| alias syri='python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")' | |
| ./example/example_workflow.sh |