Test Conda environments #2
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| name: Test Conda environments | |
| on: | |
| workflow_dispatch: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - 'tutorials/snakemake/snakefile_mrsa.smk' | |
| - 'tutorials/snakemake/environment.yml' | |
| - 'tutorials/nextflow/environment.yml' | |
| - 'tutorials/nextflow/main_mrsa.yml' | |
| - 'tutorials/nextflow/samplesheet.csv' | |
| - 'tutorials/jupyter/environment.yml' | |
| - 'tutorials/jupyter/references.bib' | |
| - 'tutorials/jupyter/supplementary_material.ipynb' | |
| - 'tutorials/quarto/environment.yml' | |
| - 'tutorials/quarto/quarto-tutorial-example.qmd' | |
| concurrency: | |
| group: conda-env-test | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| env: [snakemake, nextflow, jupyter, quarto] | |
| include: | |
| - env: snakemake | |
| cmd: snakemake -c 1 -d tutorials/snakemake/ -s tutorials/snakemake/snakefile_mrsa.smk | |
| - env: nextflow | |
| cmd: cd tutorials/nextflow && nextflow run main_mrsa.nf | |
| - env: jupyter | |
| cmd: jupyter nbconvert --to HTML tutorials/jupyter/supplementary_material.ipynb | |
| - env: quarto | |
| cmd: conda install -c conda-forge quarto && conda install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html | |
| exclude: | |
| - os: macos-latest | |
| env: snakemake | |
| - os: macos-latest | |
| env: nextflow | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Conda setup | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: ${{ matrix.env }}-env | |
| environment-file: tutorials/${{ matrix.env }}/environment.yml | |
| channel-priority: strict | |
| - name: Test ${{ matrix.env }} environment | |
| shell: bash -l {0} | |
| run: | | |
| conda list | |
| ${{ matrix.cmd }} |