export dr_output_format_valid

NAMESPACE

@@ -32,6 +32,7 @@ export(bcftools_parse_vcf_regions)
 export(date_log)
 export(dr_func_eval)
 export(dr_gds_download)
+export(dr_output_format_valid)
 export(empty_tbl)
 export(file_regex_getter)
 export(gds_file_download)

R/tidy.R

@@ -19,13 +19,14 @@
 #' \dontrun{
 #' in_dir <- paste0(
 #'   "gds://production/analysis_data/SBJ01639/tso_ctdna_tumor_only/",
-#'   "202204045ad5743c/L2200214/Results/PRJ220425_L2200214/"
+#'   "202204045ad5743c/L2200214/Results/PRJ220425_L2200214"
 #' )
-#' out_dir <- here::here("nogit/tso/2023-08-01")
-#' in_dir <- file.path(out_dir, "dracarys_gds_sync")
+#' o1 <- sub("^gds://", "", in_dir)
+#' out_dir <- file.path(fs::path_home(), "icav1/g", o1)
+#' # in_dir <- file.path(out_dir, "dracarys_gds_sync")
 #' prefix <- "SBJ01639"
 #' out_format <- "rds"
-#' umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, out_format = out_format, dryrun = F)
+#' umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, out_format = out_format, dryrun = T)
 #'
 #' in_dir <- here::here(glue("nogit/tso/2022-12-13/SBJ02858/dracarys_gds_sync"))
 #' out_dir <- file.path(in_dir, "../out")

R/utils.R

@@ -47,6 +47,10 @@ session_info_tbls <- function(pkgs = NULL) {
   )
 }
 
+#' Output Format is Valid
+#'
+#' Checks that the specified output format is valid.
+#' @export
 dr_output_format_valid <- function(x) {
   format_choices <- c("tsv", "parquet", "delta", "rds")
   assertthat::assert_that(