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| name: "Lassa workflow" | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| lassa: | |
| permissions: | |
| contents: read | |
| id-token: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: https://mrc-ide.r-universe.dev | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-dependencies: | | |
| mrc-ide/orderly.sharedfile | |
| mrc-ide/epireview | |
| - uses: mrc-ide/orderly-action@main | |
| with: | |
| packit-url: https://packit.dide.ic.ac.uk/reside | |
| - shell: Rscript {0} | |
| run: | | |
| orderly_location_pull_packet("latest(name == 'db_extraction' && parameter:pathogen == 'LASSA')", | |
| options = list(location="packit.dide")) | |
| ids <- c( | |
| orderly_run("db_double", parameters = list(pathogen = "LASSA")), | |
| orderly_run("db_compilation", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_serology", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_severity", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_delays", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_transmission", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_summary", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_latex_tables", parameters = list(pathogen = "LASSA")), | |
| orderly_run("lassa_collate", parameters = list(pathogen = "LASSA"))) | |
| orderly_location_push(ids, "packit.dide") |