Lecture updates #172
Workflow file for this run
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: 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/[email protected] | |
| 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 }} |