Merge pull request #145 from umccr/wfdragen

DRAGEN workflow support

NAMESPACE

@@ -4,37 +4,35 @@ S3method(read,File)
 export(BcftoolsStatsFile)
 export(BclconvertReports)
 export(BclconvertReports375)
-export(FastqcMetricsFile)
 export(File)
-export(FragmentLengthHistFile)
-export(MappingMetricsFile)
 export(MultiqcFile)
 export(PcgrJsonFile)
 export(PcgrTiersFile)
 export(PloidyEstimationMetricsFile)
-export(ReplayFile)
-export(SvMetricsFile)
-export(TimeMetricsFile)
-export(TrimmerMetricsFile)
-export(VCMetricsFile)
 export(Wf)
+export(Wf_dragen)
 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)
-export(WgsCoverageMetricsFile)
-export(WgsFineHistFile)
-export(WgsHistFile)
 export(bcftools_parse_vcf)
 export(bcftools_parse_vcf_regions)
 export(date_log)
 export(dr_func_eval)
 export(dr_gds_download)
 export(dr_output_format_valid)
 export(dr_s3_download)
+export(dragen_cnv_metrics_read)
+export(dragen_coverage_metrics_read)
+export(dragen_fastqc_metrics_read)
+export(dragen_gc_metrics_read)
+export(dragen_mapping_metrics_read)
+export(dragen_sv_metrics_read)
+export(dragen_trimmer_metrics_read)
+export(dragen_umi_metrics_read)
+export(dragen_vc_metrics_read)
 export(dtw_Wf_tso_ctdna_tumor_only)
 export(dtw_Wf_tso_ctdna_tumor_only_v2)
 export(empty_tbl)
@@ -69,7 +67,6 @@ export(s3_list_files_filter_relevant)
 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)

R/Wf.R

@@ -92,7 +92,8 @@ Wf <- R6::R6Class(
         "oncoanalyser_wgts_existing_both",
         "sash"
       )
-      assertthat::assert_that(wname %in% wnames)
+      subwnames <- c("dragen")
+      assertthat::assert_that(wname %in% c(wnames, subwnames))
       self$path <- sub("/$", "", path) # remove potential trailing slash
       self$wname <- wname
       self$filesystem <- dplyr::case_when(
@@ -208,6 +209,7 @@ Wf <- R6::R6Class(
     #' @param drid dracarys ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
     write = function(x, outdir = NULL, prefix = NULL, format = "tsv", drid = NULL) {
       assertthat::assert_that(!is.null(prefix))
+      assertthat::assert_that(all(c("name", "data") %in% colnames(x)))
       if (!is.null(outdir)) {
         prefix <- file.path(outdir, prefix)
       }
@@ -218,7 +220,7 @@ Wf <- R6::R6Class(
           out = list(write_dracarys(obj = .data$data, prefix = .data$p, out_format = format, drid = drid))
         ) |>
         dplyr::ungroup() |>
-        dplyr::select("name", "data")
+        dplyr::select("name", "data", prefix = "p")
       invisible(d_write)
     }
   ) # end public