Merge devel into main
#183
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: setup | |
| on: | |
| workflow_dispatch: | |
| branches: | |
| - main | |
| - devel | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| install: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ macos-latest, ubuntu-latest ] | |
| env: [snakemake, nextflow, jupyter, rmarkdown] | |
| 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: rmarkdown | |
| cmd: cd tutorials/rmarkdown && echo 'rmarkdown::render("code/supplementary_material.Rmd", output_file="supplementary.html")' | R --vanilla | |
| 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 }} |