Wf_tso_ctdna_tumor_only_v2 Download Tidy and Write — dtw_Wf_tso_ctdna_tumor_only_v2 • dracarys

Downloads files from the tso_ctdna_tumor_only_v2 workflow and writes them in a tidy format.

Usage

dtw_Wf_tso_ctdna_tumor_only_v2(
  path,
  prefix,
  outdir,
  outdir_tidy = file.path(outdir, "dracarys_tidy"),
  format = "rds",
  max_files = 1000,
  dryrun = FALSE
)

Arguments

path: Path to directory with raw workflow results (S3 or local filesystem).
prefix: The LibraryID prefix of the sample (needed for path lookup).
outdir: Path to output directory with raw files.
outdir_tidy: Path to output directory with tidy files.
format: Format of output files.
max_files: Max number of files to list.
dryrun: If TRUE, just list the files that will be downloaded (don't download them).

Value

Tibble of tidy tibbles.

Examples

if (FALSE) { # \dontrun{
p <- file.path(
  "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production",
  "analysis/cttsov2/20240915ff0295ed"
)
prefix <- "L2401290"
outdir <- sub("s3:/", "~/s3", p)
d <- dtw_Wf_tso_ctdna_tumor_only_v2(
  path = p, prefix = prefix, outdir = outdir,
  format = "tsv",
  dryrun = F
)
} # }