Reads and writes tidy versions of files from the tso_ctdna_tumor_only_v2 workflow.
Super class
dracarys::Wf -> Wf_tso_ctdna_tumor_only_v2
Methods
Method new()
Create a new Wf_tso_ctdna_tumor_only_v2 object.
Usage
Wf_tso_ctdna_tumor_only_v2$new(path = NULL, prefix = NULL)Method print()
Print details about the Workflow.
Examples
if (FALSE) { # \dontrun{
#---- Local ----#
p <- file.path(
"~/s3/pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production",
"analysis/cttsov2/20240915ff0295ed"
)
prefix <- "L2401290"
t1 <- Wf_tso_ctdna_tumor_only_v2$new(path = p, prefix = prefix)
t1$list_files(max_files = 100)
t1$list_files_filter_relevant(max_files = 300)
d <- t1$download_files(max_files = 100, dryrun = F)
d_tidy <- t1$tidy_files(d)
d_write <- t1$write(
d_tidy,
outdir = file.path(p, "dracarys_tidy"),
prefix = prefix,
format = "tsv"
)
#---- S3 ----#
p <- file.path(
"s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production",
"analysis/cttsov2/20240915ff0295ed"
)
prefix <- "L2401290"
outdir <- sub("s3:/", "~/s3", p)
t2 <- Wf_tso_ctdna_tumor_only_v2$new(path = p, prefix = prefix)
t2$list_files(max_files = 500)
t2$list_files_filter_relevant(max_files = 500)
d <- t2$download_files(
outdir = outdir,
max_files = 500,
dryrun = F
)
d_tidy <- t2$tidy_files(d)
d_write <- t2$write(
d_tidy,
outdir = file.path(outdir, "dracarys_tidy"),
prefix = prefix,
format = "tsv"
)
} # }