lassa.yaml

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")