WIP #14
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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: ./.github/actions/setup.yaml | |
| - shell: Rscript {0} | |
| run: | | |
| library(orderly2) | |
| orderly_location_pull_packet("latest(name == 'db_extraction' && parameter:pathogen == 'LASSA')", | |
| options = list(location="packit")) | |
| 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") |