Wf: fix writer

umccr · Sep 21, 2024 · 108c07f · 108c07f
1 parent bb854c2
commit 108c07f
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Showing 2 changed files with 14 additions and 7 deletions.
diff --git a/R/Wf.R b/R/Wf.R
@@ -213,12 +213,11 @@ Wf <- R6::R6Class(
       d_write <- x |>
         dplyr::rowwise() |>
         dplyr::mutate(
-          section = sub("read_", "", .data$type),
-          p = glue("{prefix}_{.data$section}"),
+          p = glue("{prefix}_{.data$name}"),
           out = list(write_dracarys(obj = .data$data, prefix = .data$p, out_format = format, drid = drid))
         ) |>
         dplyr::ungroup() |>
-        dplyr::select("section", "data") |>
+        dplyr::select("name", "data") |>
         tibble::deframe()
       invisible(d_write)
     }

diff --git a/R/tso.R b/R/tso.R
@@ -19,13 +19,21 @@
 #' 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/SBJ04651/tso_ctdna_tumor_only",
-#'   "20240223d1951163/L2400183/Results"
+#'   "gds://production/analysis_data/SBJ05563/tso_ctdna_tumor_only",
+#'   "20240914d41300cd/L2401388/Results"
 #' )
-#'
+#' SampleID <- "PRJ241446"
+#' LibraryID <- "L2401388"
+#' prefix <- glue("{SampleID}__{LibraryID}")
 #' outdir <- file.path(sub("gds:/", "~/icav1/g", p))
 #' token <- Sys.getenv("ICA_ACCESS_TOKEN")
 #' t2 <- Wf_tso_ctdna_tumor_only$new(path = p, SampleID = SampleID, LibraryID = LibraryID)
@@ -38,7 +46,7 @@
 #' d_tidy <- t2$tidy_files(d)
 #' d_write <- t2$write(
 #'   d_tidy,
-#'   outdir = file.path(p, "dracarys_tidy"),
+#'   outdir = file.path(outdir, "dracarys_tidy"),
 #'   prefix = prefix,
 #'   format = "tsv"
 #' )