Devel #177
Workflow file for this run
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| name: slim-setup | |
| on: | |
| workflow_dispatch: | |
| branches: | |
| - main | |
| - devel | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| docker-slim-install: | |
| # Install environments inside the slim container | |
| runs-on: ubuntu-latest | |
| container: | |
| nbisweden/workshop-reproducible-research:slim | |
| strategy: | |
| matrix: | |
| 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: mamba install -c conda-forge quarto && mamba install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: ${{ matrix.env }}-env | |
| environment-file: tutorials/${{ matrix.env }}/environment.yml | |
| use-mamba: true | |
| channel-priority: strict | |
| - name: Test ${{ matrix.env }} | |
| shell: bash -l {0} | |
| run: | | |
| conda list | |
| ${{ matrix.cmd }} |