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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: | |
| dependencies: NA | |
| packages: | | |
| mrc-ide/orderly.sharedfile | |
| mrc-ide/epireview | |
| cowplot | |
| doconv | |
| dplyr | |
| epitrix | |
| estmeansd | |
| flextable | |
| ftExtra | |
| ggbreak | |
| ggforce | |
| ggplot2 | |
| ggrepel | |
| ggsci | |
| ggspatial | |
| grid | |
| gridExtra | |
| gt | |
| harrypotter | |
| ids | |
| janitor | |
| meta | |
| metafor | |
| mixdist | |
| odbc | |
| officer | |
| optparse | |
| patchwork | |
| png | |
| purrr | |
| ragg | |
| readr | |
| readxl | |
| rio | |
| rnaturalearth | |
| rnaturalearthdata | |
| scales | |
| sf | |
| snakecase | |
| splitstackshape | |
| stringr | |
| tibble | |
| tidyr | |
| tidyverse | |
| tm | |
| writexl | |
| zip | |
| - uses: mrc-ide/orderly-action@main | |
| with: | |
| packit-url: https://packit.dide.ic.ac.uk/priority-pathogens | |
| - 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") | |
| - shell: Rscript {0} | |
| run: | | |
| library(orderly2) | |
| orderly_location_pull_packet("latest(name == 'db_extraction' && parameter:pathogen == 'EBOLA')", | |
| options = list(location="packit")) | |
| ids <- c( | |
| orderly_run("db_double", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("db_compilation", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_reproduction_number", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_severity", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_severity_additional", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_delays", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_seroprevalence", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_mutations", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_attack_rate", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_overdispersion", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_growth_rate", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_doubling_time", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_models", parameters = list(pathogen = "EBOLA")), | |
| orderly_run("ebola_summary", parameters = list(pathogen = "EBOLA"))) | |
| orderly_location_push(ids, "packit") |