Reads and writes tidy versions of files from the tso_ctdna_tumor_only workflow.
Super class
dracarys::Wf -> Wf_tso_ctdna_tumor_only
Methods
Method new()
Create a new Wf_tso_ctdna_tumor_only object.
Usage
Wf_tso_ctdna_tumor_only$new(path = NULL, prefix = NULL)Method print()
Print details about the Workflow.
Examples
if (FALSE) { # \dontrun{
#---- Local ----#
p <- file.path(
"~/icav1/g/production/analysis_data/SBJ04651/tso_ctdna_tumor_only",
"20240223d1951163/L2400183"
)
prefix <- "PRJ230876_L2400183"
t1 <- Wf_tso_ctdna_tumor_only$new(path = p, prefix = prefix)
t1$list_files(max_files = 20)
t1$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$write(
d_tidy,
outdir = file.path(p, "dracarys_tidy"),
prefix = prefix,
format = "tsv"
)
#---- GDS ----#
p <- file.path(
"gds://production/analysis_data/SBJ05563/tso_ctdna_tumor_only",
"20240914d41300cd/L2401388/Results"
)
prefix <- "PRJ241446_L2401388"
outdir <- file.path(sub("gds:/", "~/icav1/g", p))
token <- Sys.getenv("ICA_ACCESS_TOKEN")
t2 <- Wf_tso_ctdna_tumor_only$new(path = p, prefix = prefix)
t2$list_files(max_files = 100, ica_token = token)
t2$list_files_filter_relevant(max_files = 100, ica_token = token)
d <- t2$download_files(
outdir = outdir, ica_token = token,
max_files = 100, dryrun = F
)
d_tidy <- t2$tidy_files(d)
d_write <- t2$write(
d_tidy,
outdir = file.path(outdir, "dracarys_tidy"),
prefix = prefix,
format = "tsv"
)
} # }