Test Conda environments #3
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 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 }} |