dracarys GDS Download — dr_gds_download • dracarys

Download only GDS files that can be processed by dracarys.

Usage

dr_gds_download(
  gdsdir,
  outdir,
  token = Sys.getenv("ICA_ACCESS_TOKEN"),
  pattern = NULL,
  page_size = 100,
  dryrun = FALSE,
  regexes = DR_FILE_REGEX,
  recursive = NULL
)

Arguments

gdsdir: Full path to GDS directory.
outdir: Local output directory.
token: ICA access token (def: $ICA_ACCESS_TOKEN env var).
pattern: Pattern to further filter the returned file type tibble.
page_size: Page size (def: 10 via ICA API).
dryrun: If TRUE, just list the files that will be downloaded (don't download them).
regexes: Tibble with regex and function name (see example).
recursive: Should files be returned recursively in and under the specified GDS directory, or only directly in the specified GDS directory (def: TRUE via ICA API).

Examples

if (FALSE) { # \dontrun{
gdsdir <- "gds://production/analysis_data/SBJ01155/umccrise/202408300c218043/L2101566__L2101565"
outdir <- sub("gds:/", "~/icav1/g", gdsdir)
regexes <- tibble::tribble(
  ~regex, ~fun,
  "multiqc_data\\.json$", "MultiqcJsonFile",
  "-somatic\\.pcgr\\.json\\.gz$", "pcgrjson"
)
dr_gds_download(gdsdir = gdsdir, outdir = outdir, regexes = regexes, dryrun = T)
} # }