Downloads files from the tso_ctdna_tumor_only workflow and writes them in a tidy format.
Usage
dtw_Wf_tso_ctdna_tumor_only(
path,
prefix,
outdir,
outdir_tidy = file.path(outdir, "dracarys_tidy"),
format = "rds",
max_files = 1000,
ica_token = Sys.getenv("ICA_ACCESS_TOKEN"),
dryrun = FALSE
)Arguments
- path
Path to directory with raw workflow results (from GDS, S3, or local filesystem).
- prefix
The SubjectID_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.
- ica_token
ICA access token (def: $ICA_ACCESS_TOKEN env var).
- dryrun
If TRUE, just list the files that will be downloaded (don't download them).
Examples
if (FALSE) { # \dontrun{
p <- file.path(
"gds://production/analysis_data/SBJ05563/tso_ctdna_tumor_only",
"20240914d41300cd/L2401388/Results"
)
prefix <- "PRJ241446_L2401388"
outdir <- file.path(sub("gds:/", "~/icav1/g", p))
token <- Sys.getenv("ICA_ACCESS_TOKEN")
d <- dtw_Wf_tso_ctdna_tumor_only(
path = p, prefix = prefix, outdir = outdir,
format = "tsv",
dryrun = F
)
} # }