Merge pull request #135 from umccr/cttsov2

TSO500 ctDNA v2 support
umccr · Oct 4, 2024 · 86730fc · 86730fc
2 parents cab5811 + c1ccfe2
commit 86730fc
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Showing 38 changed files with 1,528 additions and 2,365 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,23 +16,12 @@ export(ReplayFile)
 export(SvMetricsFile)
 export(TimeMetricsFile)
 export(TrimmerMetricsFile)
-export(TsoAlignCollapseFusionCallerMetricsFile)
-export(TsoCombinedVariantOutputFile)
-export(TsoCopyNumberVariantsVcfFile)
-export(TsoFragmentLengthHistFile)
-export(TsoFusionsCsvFile)
-export(TsoMergedSmallVariantsGenomeVcfFile)
-export(TsoMergedSmallVariantsVcfFile)
-export(TsoMsiFile)
-export(TsoSampleAnalysisResultsFile)
-export(TsoTargetRegionCoverageFile)
-export(TsoTmbFile)
-export(TsoTmbTraceTsvFile)
 export(VCMetricsFile)
 export(Wf)
 export(Wf_sash)
 export(Wf_sash_download_tidy_write)
 export(Wf_tso_ctdna_tumor_only)
+export(Wf_tso_ctdna_tumor_only_v2)
 export(Wf_umccrise)
 export(Wf_umccrise_download_tidy_write)
 export(WgsContigMeanCovFile)
@@ -46,6 +35,8 @@ export(dr_func_eval)
 export(dr_gds_download)
 export(dr_output_format_valid)
 export(dr_s3_download)
+export(dtw_Wf_tso_ctdna_tumor_only)
+export(dtw_Wf_tso_ctdna_tumor_only_v2)
 export(empty_tbl)
 export(file_regex_getter)
 export(gds_file_download_api)
@@ -79,11 +70,18 @@ export(s3_search)
 export(session_info_kable)
 export(tidy_files)
 export(time_metrics_process)
+export(tso_acfc_plot)
+export(tso_acfc_read)
+export(tso_combinedvaro_smallv_read)
+export(tso_fusions_read)
+export(tso_msi_read)
+export(tso_sar_read)
+export(tso_targetregcvg_plot)
+export(tso_targetregcvg_read)
+export(tso_tmbt_read)
 export(umccr_tidy)
 export(write_dracarys_list_of_tbls)
 importFrom(R6,R6Class)
-importFrom(ggplot2,ggplot)
-importFrom(ggrepel,geom_text_repel)
 importFrom(glue,glue)
 importFrom(rlang,"!!!")
 importFrom(rlang,"%||%")

diff --git a/R/Wf.R b/R/Wf.R
@@ -79,6 +79,7 @@ Wf <- R6::R6Class(
       wnames <- c(
         "bcl_convert",
         "tso_ctdna_tumor_only",
+        "tso_ctdna_tumor_only_v2",
         "wgs_alignment_qc",
         "wts_alignment_qc",
         "wts_tumor_only",
@@ -217,8 +218,7 @@ Wf <- R6::R6Class(
           out = list(write_dracarys(obj = .data$data, prefix = .data$p, out_format = format, drid = drid))
         ) |>
         dplyr::ungroup() |>
-        dplyr::select("name", "data") |>
-        tibble::deframe()
+        dplyr::select("name", "data")
       invisible(d_write)
     }
   ) # end public

diff --git a/R/fs_icav1.R b/R/fs_icav1.R
@@ -190,8 +190,14 @@ dr_gds_download <- function(gdsdir, outdir, token = Sys.getenv("ICA_ACCESS_TOKEN
     ) |>
     dplyr::select("type", "bname", "size", "lastmodified", "file_id", "localpath", "gdspath")
   # download recognisable dracarys files to outdir/<mirrored-cloud-path>/{bname}
+  tot_size <- d |>
+    dplyr::summarise(tot_size = sum(.data$size)) |>
+    dplyr::pull(tot_size)
   if (!dryrun) {
-    cli::cli_alert_info("{date_log()} {e('arrow_heading_down')} Downloading files from {.file {gdsdir}}")
+    txt <- paste0(
+      "{e('arrow_heading_down')} {nrow(d)} files ({tot_size}): {.file {gdsdir}}\n"
+    )
+    cli::cli_alert_info(txt)
     res <- d |>
       dplyr::rowwise() |>
       dplyr::mutate(

diff --git a/R/regex.R b/R/regex.R
@@ -89,10 +89,7 @@ FILES_DOWNLOAD_BUT_IGNORE <- c(
 #' @return Evaluated function.
 #' @examples
 #' mean_1_to_10 <- dr_func_eval("mean", v = c("mean", "sd"))(1:10)
-#' x <- system.file("extdata/tso/sample705.fragment_length_hist.json.gz", package = "dracarys")
-#' obj <- dr_func_eval("TsoFragmentLengthHistFile")$new(x)
 #' @testexamples
-#' expect_equal("sample705.fragment_length_hist.json.gz", obj$bname())
 #' expect_equal(mean_1_to_10, base::mean(1:10))
 #' expect_null(dr_func_eval("foo"))
 #' @export