diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 748d2c9..b9d4ad3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.2
+    rev: v0.4.3
     hooks:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
diff --git a/NAMESPACE b/NAMESPACE
index d1e12a5..9df48ec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,6 +3,7 @@
 S3method(read,File)
 export(BcftoolsStatsFile)
 export(BclconvertReports)
+export(BclconvertReports375)
 export(FastqcMetricsFile)
 export(File)
 export(FragmentLengthHistFile)
@@ -33,7 +34,6 @@ export(UmQcSumFile)
 export(UmSigsSnvFile)
 export(VCMetricsFile)
 export(Wf)
-export(Wf_bcl_convert)
 export(Wf_tso_ctdna_tumor_only)
 export(WgsContigMeanCovFile)
 export(WgsCoverageMetricsFile)
diff --git a/R/bclconvert.R b/R/bclconvert.R
index f63d36c..c5d671a 100644
--- a/R/bclconvert.R
+++ b/R/bclconvert.R
@@ -1,47 +1,451 @@
-#' bcl_convert Wf R6 Class
+#' BclconvertReports R6 Class
 #'
 #' @description
-#' Contains methods for reading and processing files output from the UMCCR
-#' `bcl_convert` workflow.
+#' Reads and writes tidy versions of files within the `Reports` directory output
+#' from BCLConvert v4.2.7. See the DRAGEN v4.2 documentation at
+#' https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/OutputFiles.htm.
 #'
 #' @examples
 #' \dontrun{
-#' indir <- file.path()
-#' sample_id <- "PTC_ctTSO240429"
-#' library_id <- "L2400482"
-#' d <- TsoCombinedVariantOutputFile$new(x)
-#' d$read()
+#' p1 <- "240816_A01052_0220_AHM7VHDSXC/202408195d4f2fc4/Reports"
+#' b <- here::here("nogit/bcl_convert", p1) |>
+#'   BclconvertReports$new()
+#' b$path
+#' b$contents
+#' d <- b$read()
+#' b$write(d, out_dir = tempdir(), prefix = "sampleA", out_format = "tsv")
 #' }
+#'
 #' @export
-Wf_bcl_convert <- R6::R6Class(
-  "Wf_bcl_convert",
+BclconvertReports <- R6::R6Class(
+  "BclconvertReports",
   public = list(
-    #' @field indir Input directory containing Reports per assay type
-    #' (e.g. /primary_data/240607_A01052_0209_BHLHFTDSXC/2024061140802544/).
-    indir = NULL,
-
-    #' @description Create a new Wf_bcl_convert object.
-    #' @param indir Input directory containing Reports per assay type.
-    initialize = function(indir) {
-      self$indir <- indir
+    #' @field path Path to the `Reports` directory.
+    #' @field contents Tibble with file path, basename, and size.
+    path = NULL,
+    contents = NULL,
+    #' @description Create a new BclconvertReports object.
+    #' @param path Path to the `Reports` directory.
+    initialize = function(path = NULL) {
+      stopifnot(is.character(path), length(path) == 1)
+      self$path <- normalizePath(path)
+      self$contents <- fs::dir_info(path) |>
+        dplyr::mutate(
+          bname = basename(.data$path),
+          size = as.character(trimws(.data$size))
+        ) |>
+        dplyr::select("path", "bname", "size")
     },
-    #' @description Print details about the Workflow
+    #' @description Print details about the BclconvertReports directory.
     #' @param ... (ignored).
     print = function(...) {
+      bnames <- self$contents |>
+        dplyr::mutate(
+          low = tolower(.data$bname),
+        ) |>
+        dplyr::arrange(.data$low) |>
+        dplyr::mutate(
+          n = dplyr::row_number(),
+          bn = glue("{.data$n}. {.data$bname} ({.data$size})")
+        ) |>
+        dplyr::pull("bn")
+      cat("#--- BclconvertReports ---#\n")
+      cat(glue("Path: {self$path}"), "\n")
+      cat("Contents:\n")
+      cat(bnames, sep = "\n")
+      invisible(self)
+    },
+
+    #' @description Read Adapter_Cycle_Metrics.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - read: read number.
+    #' - cycle: cycle number.
+    #' - cluster_n: number of clusters where the adapter was detected
+    #'   to begin precisely at this cycle.
+    #' - cluster_pct: percentage of all clusters where the adapter was detected
+    #'   to begin precisely at this cycle.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Adapter_Cycle_Metrics.csv file.
+    read_adaptercyclemetrics = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "Sample_ID", "index", "index2", "ReadNumber", "Cycle",
+          "NumClustersWithAdapterAtCycle", "% At Cycle"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "read", "cycle",
+          "cluster_n", "cluster_pct"
+        )
+      )
+      ctypes <- list(
+        old = "ccccccdd",
+        new = "cccccdd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "Sample_ID") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Adapter_Metrics.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - readnum: read number.
+    #' - adapter_bases: total number of bases trimmed as adapter from the read.
+    #' - sample_bases: total number of bases not trimmed from the read.
+    #' - adapter_bases_pct: percentage of bases trimmed as adapter from the read.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Adapter_Metrics.csv file.
+    read_adaptermetrics = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "Sample_ID", "index", "index2", "ReadNumber",
+          "AdapterBases", "SampleBases", "% Adapter Bases"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "readnum", "adapter_bases",
+          "sample_bases", "adapter_bases_pct"
+        )
+      )
+      ctypes <- list(
+        old = "cccccddd",
+        new = "ccccddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = ifelse(
+          is.na(.data$index), NA_character_, paste0(.data$index, "-", .data$index2)
+        )) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "Sample_ID") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Demultiplex_Stats.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - reads_n: total number of pass-filter reads mapping to this sample for the lane.
+    #' - perfect_idxreads_n: number of mapped reads with barcodes matching the indexes exactly.
+    #' - one_mismatch_idxreads_n: number of mapped reads with barcodes matched with one base mismatched.
+    #' - two_mismatch_idxreads_n: number of mapped reads with barcodes matched with two bases mismatched.
+    #' - reads_pct: percentage of pass-filter reads mapping to this sample for the lane.
+    #' - perfect_idxreads_pct: percentage of mapped reads with barcodes matching the indexess exactly.
+    #' - one_mismatch_idxreads_pct: percentage of mapped reads with one mismatch to the indexes.
+    #' - two_mismatch_idxreads_pct: percentage of mapped reads with two mismatches to the indexes.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Demultiplex_Stats.csv file.
+    read_demultiplexstats = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "SampleID", "Index", "# Reads", "# Perfect Index Reads",
+          "# One Mismatch Index Reads", "# Two Mismatch Index Reads",
+          "% Reads", "% Perfect Index Reads", "% One Mismatch Index Reads",
+          "% Two Mismatch Index Reads"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "reads_n", "perfect_idxreads_n",
+          "one_mismatch_idxreads_n", "two_mismatch_idxreads_n",
+          "reads_pct", "perfect_idxreads_pct",
+          "one_mismatch_idxreads_pct", "two_mismatch_idxreads_pct"
+        )
+      )
+      ctypes <- list(
+        old = "cccdddddddd",
+        new = "cccdddddddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Demultiplex_Tile_Stats.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - tile: tile number.
+    #' - reads_n: total number of pass-filter reads mapping to this sample for the lane.
+    #' - reads_pct: percentage of pass-filter reads mapping to this sample for the lane.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Demultiplex_Tile_Stats.csv file.
+    read_demultiplextilestats = function(x) {
+      cnames <- list(
+        old = c("Lane", "SampleID", "Index", "Tile", "# Reads", "% Reads"),
+        new = c("lane", "sampleid", "indexes", "tile", "reads_n", "reads_pct")
+      )
+      ctypes <- list(
+        old = "ccccdd",
+        new = "ccccdd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Quality_Metrics.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - readnum: read number (1 or 2).
+    #' - yield: number of bases mapping.
+    #' - yieldq30: number of bases with quality score >= 30 mapping.
+    #' - qscore_sum: sum of quality scores of bases mapping.
+    #' - qscore_mean_pf: mean quality score of bases mapping.
+    #' - q30_pct: percentage of bases with quality score >= 30 mapping.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Quality_Metrics.csv file.
+    read_qualitymetrics = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "SampleID", "index", "index2", "ReadNumber", "Yield",
+          "YieldQ30", "QualityScoreSum", "Mean Quality Score (PF)", "% Q30"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "readnum", "yield",
+          "yieldq30", "qscore_sum", "qscore_mean_pf", "q30_pct"
+        )
+      )
+      ctypes <- list(
+        old = "cccccddddd",
+        new = "ccccddddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "SampleID") |>
+        rlang::set_names(cnames$new)
+    },
+
+
+    #' @description Read Quality_Tile_Metrics.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - readnum: read number (1 or 2).
+    #' - tile: tile number.
+    #' - yield: number of bases mapping.
+    #' - yieldq30: number of bases with quality score >= 30 mapping.
+    #' - qscore_sum: sum of quality scores of bases mapping.
+    #' - qscore_mean_pf: mean quality score of bases mapping.
+    #' - q30_pct: percentage of bases with quality score >= 30 mapping.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Quality_Tile_Metrics.csv file.
+    read_qualitytilemetrics = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "SampleID", "index", "index2", "ReadNumber", "Tile", "Yield",
+          "YieldQ30", "QualityScoreSum", "Mean Quality Score (PF)", "% Q30"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "readnum", "tile", "yield",
+          "yieldq30", "qscore_sum", "qscore_mean_pf", "q30_pct"
+        )
+      )
+      ctypes <- list(
+        old = "ccccccddddd",
+        new = "cccccddddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "SampleID") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Index_Hopping_Counts.csv file.
+    #'
+    #' - lane: lane number.
+    #' - sampleid: sample ID from sample sheet.
+    #' - indexes: index/index2 from sample sheet for this sample.
+    #' - reads_n: total number of pass-filter reads mapping to the indexes.
+    #' - reads_hopped_pct: percentage of hopped pass-filter reads mapping to the indexes.
+    #' - reads_pct: percentage of all pass-filter reads mapping to the indexes.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Index_Hopping_Counts.csv file.
+    read_indexhoppingcounts = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "SampleID", "index", "index2", "# Reads",
+          "% of Hopped Reads", "% of All Reads"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes",
+          "reads_n", "reads_hopped_pct", "reads_pct"
+        )
+      )
+      ctypes <- list(
+        old = "ccccd",
+        new = "cccddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "SampleID") |>
+        rlang::set_names(cnames$new)
+    },
 
+    #' @description Read Top_Unknown_Barcodes.csv file.
+    #'
+    #' - lane: lane number.
+    #' - indexes: index/index2 of this unlisted sequence.
+    #' - reads_n: total number of pass-filter reads mapping to the indexes.
+    #' - unknownbcodes_pct: percentage of unknown pass-filter reads mapping to the indexes.
+    #' @param x (`character(1)`)\cr
+    #'   Path to Top_Unknown_Barcodes.csv file.
+    read_topunknownbarcodes = function(x) {
+      cnames <- list(
+        old = c("Lane", "index", "index2", "# Reads", "% of Unknown Barcodes", "% of All Reads"),
+        new = c("lane", "indexes", "reads_n", "unknownbcodes_pct", "reads_pct")
+      )
+      ctypes <- list(
+        old = "cccddd",
+        new = "ccddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "Lane") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read fastq_list.csv file.
+    #'
+    #' - rgid: read group.
+    #' - rgsm: sample ID.
+    #' - rglb: library.
+    #' - lane: flow cell lane.
+    #' - readnum: read number (1 or 2).
+    #' - filepath: path to the FASTQ file.
+    #' @param x (`character(1)`)\cr
+    #'   Path to fastq_list.csv file.
+    read_fastqlist = function(x) {
+      cnames <- list(
+        old = c("RGID", "RGSM", "RGLB", "Lane", "Read1File", "Read2File"),
+        new = c("rgid", "rgsm", "rglb", "lane", "readnum", "filepath")
+      )
+      ctypes <- list(
+        old = c("cccccc"),
+        new = c("cccccc")
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        tidyr::pivot_longer(c("Read1File", "Read2File"), names_to = "readnum", values_to = "filepath") |>
+        dplyr::mutate(readnum = sub("Read(.)File", "\\1", .data$readnum)) |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description
+    #' Reads contents of `Reports` directory output by BCLConvert.
+    #'
+    #' @return A list of tibbles.
+    #' @export
+    read = function() {
+      # now return all as list elements
+      p <- self$path
+      list(
+        adapter_cycle_metrics = self$read_adaptercyclemetrics(file.path(p, "Adapter_Cycle_Metrics.csv")),
+        adapter_metrics = self$read_adaptermetrics(file.path(p, "Adapter_Metrics.csv")),
+        demultiplex_stats = self$read_demultiplexstats(file.path(p, "Demultiplex_Stats.csv")),
+        demultiplex_tile_stats = self$read_demultiplextilestats(file.path(p, "Demultiplex_Tile_Stats.csv")),
+        quality_metrics = self$read_qualitymetrics(file.path(p, "Quality_Metrics.csv")),
+        quality_tile_metrics = self$read_qualitytilemetrics(file.path(p, "Quality_Tile_Metrics.csv")),
+        index_hopping_counts = self$read_indexhoppingcounts(file.path(p, "Index_Hopping_Counts.csv")),
+        top_unknown_barcodes = self$read_topunknownbarcodes(file.path(p, "Top_Unknown_Barcodes.csv")),
+        fastq_list = self$read_fastqlist(file.path(p, "fastq_list.csv"))
+      )
+    },
+
+    #' @description
+    #' Writes tidied contents of `Reports` directory output by BCLConvert.
+    #'
+    #' @param d Parsed object from `self$read()`.
+    #' @param prefix Prefix of output file(s).
+    #' @param out_dir Output directory.
+    #' @param out_format Format of output file(s).
+    #' @param drid dracarys ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
+    write = function(d, out_dir = NULL, prefix, out_format = "tsv", drid = NULL) {
+      if (!is.null(out_dir)) {
+        prefix <- file.path(out_dir, prefix)
+      }
+      d_write <- d |>
+        tibble::enframe(name = "section") |>
+        dplyr::rowwise() |>
+        dplyr::mutate(
+          section_low = tolower(.data$section),
+          p = glue("{prefix}_{.data$section_low}"),
+          out = list(write_dracarys(obj = .data$value, prefix = .data$p, out_format = out_format, drid = drid))
+        ) |>
+        dplyr::ungroup() |>
+        dplyr::select("section", "value") |>
+        tibble::deframe()
+      invisible(d_write)
     }
   )
 )
 
-#' BclconvertReports R6 Class
+#' BclconvertReports375 R6 Class
 #'
 #' @description
 #' Reads and writes tidy versions of files within the `Reports` directory output
-#' from BCLConvert.
+#' from BCLConvert v4.2.7. See the DRAGEN v4.2 documentation at
+#' https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/OutputFiles.htm.
 #'
 #' @examples
 #' \dontrun{
-#' b <- BclconvertReports$new(here::here("nogit/bcl_convert/WGS_TsqNano/Reports"))
+#' p1 <- "nogit/bcl_convert/WGS_TsqNano/Reports"
+#' b <- here::here(p1) |>
+#'   BclconvertReports375$new()
 #' b$path
 #' b$contents
 #' d <- b$read()
@@ -49,14 +453,14 @@ Wf_bcl_convert <- R6::R6Class(
 #' }
 #'
 #' @export
-BclconvertReports <- R6::R6Class(
-  "BclconvertReports",
+BclconvertReports375 <- R6::R6Class(
+  "BclconvertReports375",
   public = list(
     #' @field path Path to the `Reports` directory.
     #' @field contents Tibble with file path, basename, and size.
     path = NULL,
     contents = NULL,
-    #' @description Create a new BclconvertReports object.
+    #' @description Create a new BclconvertReports375 object.
     #' @param path Path to the `Reports` directory.
     initialize = function(path = NULL) {
       stopifnot(is.character(path), length(path) == 1)
@@ -68,7 +472,7 @@ BclconvertReports <- R6::R6Class(
         ) |>
         dplyr::select("path", "bname", "size")
     },
-    #' @description Print details about the BclconvertReports directory.
+    #' @description Print details about the BclconvertReports375 directory.
     #' @param ... (ignored).
     print = function(...) {
       bnames <- self$contents |>
@@ -88,104 +492,162 @@ BclconvertReports <- R6::R6Class(
       invisible(self)
     },
 
+    #' @description Read Adapter_Metrics.csv file.
+    #'
+    #' @param x (`character(1)`)\cr
+    #'   Path to Adapter_Metrics.csv file.
+    read_adaptermetrics = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "Sample_ID", "index", "index2", "R1_AdapterBases",
+          "R1_SampleBases", "R2_AdapterBases", "R2_SampleBases", "# Reads"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "adapter_bases_r1", "sample_bases_r1",
+          "adapter_bases_r2", "sample_bases_r2", "reads_n"
+        )
+      )
+      ctypes <- list(
+        old = "ccccddddd",
+        new = "cccddddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = ifelse(
+          is.na(.data$index), NA_character_, paste0(.data$index, "-", .data$index2)
+        )) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "Sample_ID") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Demultiplex_Stats.csv file.
+    #'
+    #' @param x (`character(1)`)\cr
+    #'   Path to Demultiplex_Stats.csv file.
+    read_demultiplexstats = function(x) {
+      cnames <- list(
+        old = c(
+          "Lane", "SampleID", "Index", "# Reads", "# Perfect Index Reads",
+          "# One Mismatch Index Reads", "# of >= Q30 Bases (PF)",
+          "Mean Quality Score (PF)"
+        ),
+        new = c(
+          "lane", "sampleid", "indexes", "reads_n", "perfect_idxreads_n",
+          "one_mismatch_idxreads_n", "q30_bases_n", "qscore_mean_pf"
+        )
+      )
+      ctypes <- list(
+        old = "cccddddd",
+        new = "cccddddd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Index_Hopping_Counts.csv file.
+    #'
+    #' @param x (`character(1)`)\cr
+    #'   Path to Index_Hopping_Counts.csv file.
+    read_indexhoppingcounts = function(x) {
+      cnames <- list(
+        old = c("Lane", "SampleID", "index", "index2", "# Reads"),
+        new = c("lane", "sampleid", "indexes", "reads_n")
+      )
+      ctypes <- list(
+        old = "ccccd",
+        new = "cccd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "SampleID") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read Top_Unknown_Barcodes.csv file.
+    #'
+    #' @param x (`character(1)`)\cr
+    #'   Path to Top_Unknown_Barcodes.csv file.
+    read_topunknownbarcodes = function(x) {
+      cnames <- list(
+        old = c("Lane", "index", "index2", "# Reads"),
+        new = c("lane", "indexes", "reads_n")
+      )
+      ctypes <- list(
+        old = "cccd",
+        new = "ccd"
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        dplyr::mutate(indexes = paste0(.data$index, "-", .data$index2)) |>
+        dplyr::select(-c("index", "index2")) |>
+        dplyr::relocate("indexes", .after = "Lane") |>
+        rlang::set_names(cnames$new)
+    },
+
+    #' @description Read fastq_list.csv file.
+    #'
+    #' - rgid: read group.
+    #' - rgsm: sample ID.
+    #' - rglb: library.
+    #' - lane: flow cell lane.
+    #' - readnum: read number (1 or 2).
+    #' - filepath: path to the FASTQ file.
+    #' @param x (`character(1)`)\cr
+    #'   Path to fastq_list.csv file.
+    read_fastqlist = function(x) {
+      cnames <- list(
+        old = c("RGID", "RGSM", "RGLB", "Lane", "Read1File", "Read2File"),
+        new = c("rgid", "rgsm", "rglb", "lane", "readnum", "filepath")
+      )
+      ctypes <- list(
+        old = c("cccccc"),
+        new = c("cccccc")
+      )
+      if (!file.exists(x)) {
+        return(empty_tbl(cnames$new, ctypes$new))
+      }
+      d <- readr::read_csv(x, col_types = ctypes$old)
+      assertthat::assert_that(all(colnames(d) == cnames$old))
+      d |>
+        tidyr::pivot_longer(c("Read1File", "Read2File"), names_to = "readnum", values_to = "filepath") |>
+        dplyr::mutate(readnum = sub("Read(.)File", "\\1", .data$readnum)) |>
+        rlang::set_names(cnames$new)
+    },
+
     #' @description
     #' Reads contents of `Reports` directory output by BCLConvert.
     #'
     #' @return A list of tibbles.
     #' @export
     read = function() {
+      # now return all as list elements
       p <- self$path
-      req_fnames <- c(
-        "Adapter_Metrics.csv", "Demultiplex_Stats.csv",
-        "Index_Hopping_Counts.csv", "Top_Unknown_Barcodes.csv"
-      )
-      assertthat::assert_that(
-        all(req_fnames %in% self$contents[["bname"]])
-      )
-      .read_topunknownbarcodes <- function(x) {
-        d <- readr::read_csv(x, col_types = "cccd")
-        assertthat::assert_that(all(colnames(d) == c("Lane", "index", "index2", "# Reads")))
-        d |>
-          rlang::set_names(c("lane", "index1", "index2", "n_reads")) |>
-          dplyr::mutate(barcode = glue("{.data$index1}-{.data$index2}") |> as.character()) |>
-          dplyr::select("lane", "barcode", "n_reads")
-      }
-      .read_adaptermetrics <- function(x) {
-        d <- readr::read_csv(x, col_types = "ccccddddd")
-        old_nms <- c(
-          "Lane", "Sample_ID", "index", "index2", "R1_AdapterBases",
-          "R1_SampleBases", "R2_AdapterBases", "R2_SampleBases", "# Reads"
-        )
-        assertthat::assert_that(all(colnames(d) == old_nms))
-        d |>
-          dplyr::rename(
-            index1 = "index", n_reads = "# Reads", SampleID = "Sample_ID", lane = "Lane"
-          ) |>
-          dplyr::mutate(barcode = ifelse(
-            is.na(.data$index1), NA_character_, glue("{.data$index1}-{.data$index2}")
-          )) |>
-          dplyr::select(
-            "lane", "SampleID", "barcode", "n_reads",
-            "R1_AdapterBases", "R2_AdapterBases",
-            "R1_SampleBases", "R2_SampleBases"
-          )
-      }
-      .read_indexhoppingcounts <- function(x) {
-        d <- readr::read_csv(x, col_types = "ccccd")
-        old_nms <- c("Lane", "SampleID", "index", "index2", "# Reads")
-        assertthat::assert_that(all(colnames(d) == old_nms))
-        d |>
-          dplyr::rename(index1 = "index", n_reads = "# Reads", lane = "Lane") |>
-          dplyr::mutate(barcode = glue("{.data$index1}-{.data$index2}")) |>
-          dplyr::select("lane", "SampleID", "barcode", "n_reads")
-      }
-      .read_demultiplexstats <- function(x) {
-        nms <- tibble::tribble(
-          ~new_nm, ~old_nm, ~class,
-          "lane", "Lane", "c",
-          "SampleID", "SampleID", "c",
-          "barcode", "Index", "c",
-          "n_reads", "# Reads", "d",
-          "n_perfect_idxreads", "# Perfect Index Reads", "d",
-          "n_one_mismatch_idxreads", "# One Mismatch Index Reads", "d",
-          "n_q30_bases", "# of >= Q30 Bases (PF)", "d",
-          "mean_quality_score", "Mean Quality Score (PF)", "d"
-        )
-        lookup <- tibble::deframe(nms[c("new_nm", "old_nm")])
-        d <- readr::read_csv(x, col_types = nms[["class"]])
-        assertthat::assert_that(all(colnames(d) == nms[["old_nm"]]))
-        d |>
-          dplyr::rename(dplyr::all_of(lookup))
-      }
-      .read_fastqlist <- function(x) {
-        nms <- tibble::tribble(
-          ~new_nm, ~old_nm, ~class,
-          "rgid", "RGID", "c",
-          "rgsm", "RGSM", "c",
-          "rglb", "RGLB", "c",
-          "lane", "Lane", "c",
-          "1", "Read1File", "c",
-          "2", "Read2File", "c"
-        )
-        lookup <- tibble::deframe(nms[c("new_nm", "old_nm")])
-        d <- readr::read_csv(x, col_types = readr::cols(.default = "c"))
-        assertthat::assert_that(all(colnames(d) == nms[["old_nm"]]))
-        d |>
-          dplyr::rename(dplyr::all_of(lookup)) |>
-          tidyr::pivot_longer(c("1", "2"), names_to = "read", values_to = "path")
-      }
-
-      am <- .read_adaptermetrics(file.path(p, "Adapter_Metrics.csv"))
-      ds <- .read_demultiplexstats(file.path(p, "Demultiplex_Stats.csv"))
-      ih <- .read_indexhoppingcounts(file.path(p, "Index_Hopping_Counts.csv"))
-      ub <- .read_topunknownbarcodes(file.path(p, "Top_Unknown_Barcodes.csv"))
-      fq <- .read_fastqlist(file.path(p, "fastq_list.csv"))
       list(
-        adapter_metrics = am,
-        demultiplex_stats = ds,
-        index_hopping_counts = ih,
-        top_unknown_barcodes = ub,
-        fastq_list = fq
+        adapter_metrics = self$read_adaptermetrics(file.path(p, "Adapter_Metrics.csv")),
+        demultiplex_stats = self$read_demultiplexstats(file.path(p, "Demultiplex_Stats.csv")),
+        index_hopping_counts = self$read_indexhoppingcounts(file.path(p, "Index_Hopping_Counts.csv")),
+        top_unknown_barcodes = self$read_topunknownbarcodes(file.path(p, "Top_Unknown_Barcodes.csv")),
+        fastq_list = self$read_fastqlist(file.path(p, "fastq_list.csv"))
       )
     },
 
diff --git a/inst/rmd/umccr_workflows/alignment_qc/dl_and_tidy.R b/inst/rmd/umccr_workflows/alignment_qc/dl_and_tidy.R
index 4159a2a..9a5f75f 100755
--- a/inst/rmd/umccr_workflows/alignment_qc/dl_and_tidy.R
+++ b/inst/rmd/umccr_workflows/alignment_qc/dl_and_tidy.R
@@ -5,12 +5,9 @@
   require(dracarys, include.only = "umccr_tidy")
   require(glue, include.only = "glue")
   require(here, include.only = "here")
-  require(rportal, include.only = c("awsvault_profile"))
+  require(rportal, include.only = c("portaldb_query_workflow"))
 }
 
-# log into aws umccr prod account
-rportal::awsvault_profile("upro")
-
 query_workflow_alignqc <- function(start_date) {
   wfs <- c("wgs_alignment_qc", "wts_alignment_qc") |>
     shQuote() |>
diff --git a/man/BclconvertReports.Rd b/man/BclconvertReports.Rd
index 15aae0a..47b0f6c 100644
--- a/man/BclconvertReports.Rd
+++ b/man/BclconvertReports.Rd
@@ -5,11 +5,14 @@
 \title{BclconvertReports R6 Class}
 \description{
 Reads and writes tidy versions of files within the \code{Reports} directory output
-from BCLConvert.
+from BCLConvert v4.2.7. See the DRAGEN v4.2 documentation at
+https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/OutputFiles.htm.
 }
 \examples{
 \dontrun{
-b <- BclconvertReports$new(here::here("nogit/bcl_convert/WGS_TsqNano/Reports"))
+p1 <- "240816_A01052_0220_AHM7VHDSXC/202408195d4f2fc4/Reports"
+b <- here::here("nogit/bcl_convert", p1) |>
+  BclconvertReports$new()
 b$path
 b$contents
 d <- b$read()
@@ -31,6 +34,15 @@ b$write(d, out_dir = tempdir(), prefix = "sampleA", out_format = "tsv")
 \itemize{
 \item \href{#method-BclconvertReports-new}{\code{BclconvertReports$new()}}
 \item \href{#method-BclconvertReports-print}{\code{BclconvertReports$print()}}
+\item \href{#method-BclconvertReports-read_adaptercyclemetrics}{\code{BclconvertReports$read_adaptercyclemetrics()}}
+\item \href{#method-BclconvertReports-read_adaptermetrics}{\code{BclconvertReports$read_adaptermetrics()}}
+\item \href{#method-BclconvertReports-read_demultiplexstats}{\code{BclconvertReports$read_demultiplexstats()}}
+\item \href{#method-BclconvertReports-read_demultiplextilestats}{\code{BclconvertReports$read_demultiplextilestats()}}
+\item \href{#method-BclconvertReports-read_qualitymetrics}{\code{BclconvertReports$read_qualitymetrics()}}
+\item \href{#method-BclconvertReports-read_qualitytilemetrics}{\code{BclconvertReports$read_qualitytilemetrics()}}
+\item \href{#method-BclconvertReports-read_indexhoppingcounts}{\code{BclconvertReports$read_indexhoppingcounts()}}
+\item \href{#method-BclconvertReports-read_topunknownbarcodes}{\code{BclconvertReports$read_topunknownbarcodes()}}
+\item \href{#method-BclconvertReports-read_fastqlist}{\code{BclconvertReports$read_fastqlist()}}
 \item \href{#method-BclconvertReports-read}{\code{BclconvertReports$read()}}
 \item \href{#method-BclconvertReports-write}{\code{BclconvertReports$write()}}
 \item \href{#method-BclconvertReports-clone}{\code{BclconvertReports$clone()}}
@@ -71,6 +83,254 @@ Print details about the BclconvertReports directory.
 }
 }
 \if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_adaptercyclemetrics"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_adaptercyclemetrics}{}}}
+\subsection{Method \code{read_adaptercyclemetrics()}}{
+Read Adapter_Cycle_Metrics.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item read: read number.
+\item cycle: cycle number.
+\item cluster_n: number of clusters where the adapter was detected
+to begin precisely at this cycle.
+\item cluster_pct: percentage of all clusters where the adapter was detected
+to begin precisely at this cycle.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_adaptercyclemetrics(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Adapter_Cycle_Metrics.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_adaptermetrics"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_adaptermetrics}{}}}
+\subsection{Method \code{read_adaptermetrics()}}{
+Read Adapter_Metrics.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item readnum: read number.
+\item adapter_bases: total number of bases trimmed as adapter from the read.
+\item sample_bases: total number of bases not trimmed from the read.
+\item adapter_bases_pct: percentage of bases trimmed as adapter from the read.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_adaptermetrics(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Adapter_Metrics.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_demultiplexstats"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_demultiplexstats}{}}}
+\subsection{Method \code{read_demultiplexstats()}}{
+Read Demultiplex_Stats.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item reads_n: total number of pass-filter reads mapping to this sample for the lane.
+\item perfect_idxreads_n: number of mapped reads with barcodes matching the indexes exactly.
+\item one_mismatch_idxreads_n: number of mapped reads with barcodes matched with one base mismatched.
+\item two_mismatch_idxreads_n: number of mapped reads with barcodes matched with two bases mismatched.
+\item reads_pct: percentage of pass-filter reads mapping to this sample for the lane.
+\item perfect_idxreads_pct: percentage of mapped reads with barcodes matching the indexess exactly.
+\item one_mismatch_idxreads_pct: percentage of mapped reads with one mismatch to the indexes.
+\item two_mismatch_idxreads_pct: percentage of mapped reads with two mismatches to the indexes.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_demultiplexstats(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Demultiplex_Stats.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_demultiplextilestats"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_demultiplextilestats}{}}}
+\subsection{Method \code{read_demultiplextilestats()}}{
+Read Demultiplex_Tile_Stats.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item tile: tile number.
+\item reads_n: total number of pass-filter reads mapping to this sample for the lane.
+\item reads_pct: percentage of pass-filter reads mapping to this sample for the lane.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_demultiplextilestats(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Demultiplex_Tile_Stats.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_qualitymetrics"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_qualitymetrics}{}}}
+\subsection{Method \code{read_qualitymetrics()}}{
+Read Quality_Metrics.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item readnum: read number (1 or 2).
+\item yield: number of bases mapping.
+\item yieldq30: number of bases with quality score >= 30 mapping.
+\item qscore_sum: sum of quality scores of bases mapping.
+\item qscore_mean_pf: mean quality score of bases mapping.
+\item q30_pct: percentage of bases with quality score >= 30 mapping.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_qualitymetrics(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Quality_Metrics.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_qualitytilemetrics"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_qualitytilemetrics}{}}}
+\subsection{Method \code{read_qualitytilemetrics()}}{
+Read Quality_Tile_Metrics.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item readnum: read number (1 or 2).
+\item tile: tile number.
+\item yield: number of bases mapping.
+\item yieldq30: number of bases with quality score >= 30 mapping.
+\item qscore_sum: sum of quality scores of bases mapping.
+\item qscore_mean_pf: mean quality score of bases mapping.
+\item q30_pct: percentage of bases with quality score >= 30 mapping.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_qualitytilemetrics(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Quality_Tile_Metrics.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_indexhoppingcounts"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_indexhoppingcounts}{}}}
+\subsection{Method \code{read_indexhoppingcounts()}}{
+Read Index_Hopping_Counts.csv file.
+\itemize{
+\item lane: lane number.
+\item sampleid: sample ID from sample sheet.
+\item indexes: index/index2 from sample sheet for this sample.
+\item reads_n: total number of pass-filter reads mapping to the indexes.
+\item reads_hopped_pct: percentage of hopped pass-filter reads mapping to the indexes.
+\item reads_pct: percentage of all pass-filter reads mapping to the indexes.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_indexhoppingcounts(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Index_Hopping_Counts.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_topunknownbarcodes"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_topunknownbarcodes}{}}}
+\subsection{Method \code{read_topunknownbarcodes()}}{
+Read Top_Unknown_Barcodes.csv file.
+\itemize{
+\item lane: lane number.
+\item indexes: index/index2 of this unlisted sequence.
+\item reads_n: total number of pass-filter reads mapping to the indexes.
+\item unknownbcodes_pct: percentage of unknown pass-filter reads mapping to the indexes.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_topunknownbarcodes(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Top_Unknown_Barcodes.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports-read_fastqlist"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports-read_fastqlist}{}}}
+\subsection{Method \code{read_fastqlist()}}{
+Read fastq_list.csv file.
+\itemize{
+\item rgid: read group.
+\item rgsm: sample ID.
+\item rglb: library.
+\item lane: flow cell lane.
+\item readnum: read number (1 or 2).
+\item filepath: path to the FASTQ file.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports$read_fastqlist(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to fastq_list.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-BclconvertReports-read"></a>}}
 \if{latex}{\out{\hypertarget{method-BclconvertReports-read}{}}}
 \subsection{Method \code{read()}}{
diff --git a/man/BclconvertReports375.Rd b/man/BclconvertReports375.Rd
new file mode 100644
index 0000000..01aba8b
--- /dev/null
+++ b/man/BclconvertReports375.Rd
@@ -0,0 +1,240 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bclconvert.R
+\name{BclconvertReports375}
+\alias{BclconvertReports375}
+\title{BclconvertReports375 R6 Class}
+\description{
+Reads and writes tidy versions of files within the \code{Reports} directory output
+from BCLConvert v4.2.7. See the DRAGEN v4.2 documentation at
+https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/OutputFiles.htm.
+}
+\examples{
+\dontrun{
+p1 <- "240816_A01052_0220_AHM7VHDSXC/202408195d4f2fc4/Reports"
+b <- here::here("nogit/bcl_convert", p1) |>
+  BclconvertReports375$new()
+b$path
+b$contents
+d <- b$read()
+b$write(d, out_dir = tempdir(), prefix = "sampleA", out_format = "tsv")
+}
+
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{path}}{Path to the \code{Reports} directory.}
+
+\item{\code{contents}}{Tibble with file path, basename, and size.}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-BclconvertReports375-new}{\code{BclconvertReports375$new()}}
+\item \href{#method-BclconvertReports375-print}{\code{BclconvertReports375$print()}}
+\item \href{#method-BclconvertReports375-read_adaptermetrics}{\code{BclconvertReports375$read_adaptermetrics()}}
+\item \href{#method-BclconvertReports375-read_demultiplexstats}{\code{BclconvertReports375$read_demultiplexstats()}}
+\item \href{#method-BclconvertReports375-read_indexhoppingcounts}{\code{BclconvertReports375$read_indexhoppingcounts()}}
+\item \href{#method-BclconvertReports375-read_topunknownbarcodes}{\code{BclconvertReports375$read_topunknownbarcodes()}}
+\item \href{#method-BclconvertReports375-read_fastqlist}{\code{BclconvertReports375$read_fastqlist()}}
+\item \href{#method-BclconvertReports375-read}{\code{BclconvertReports375$read()}}
+\item \href{#method-BclconvertReports375-write}{\code{BclconvertReports375$write()}}
+\item \href{#method-BclconvertReports375-clone}{\code{BclconvertReports375$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-new"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-new}{}}}
+\subsection{Method \code{new()}}{
+Create a new BclconvertReports375 object.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$new(path = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{path}}{Path to the \code{Reports} directory.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-print"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-print}{}}}
+\subsection{Method \code{print()}}{
+Print details about the BclconvertReports375 directory.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$print(...)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{...}}{(ignored).}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read_adaptermetrics"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read_adaptermetrics}{}}}
+\subsection{Method \code{read_adaptermetrics()}}{
+Read Adapter_Metrics.csv file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read_adaptermetrics(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Adapter_Metrics.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read_demultiplexstats"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read_demultiplexstats}{}}}
+\subsection{Method \code{read_demultiplexstats()}}{
+Read Demultiplex_Stats.csv file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read_demultiplexstats(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Demultiplex_Stats.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read_indexhoppingcounts"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read_indexhoppingcounts}{}}}
+\subsection{Method \code{read_indexhoppingcounts()}}{
+Read Index_Hopping_Counts.csv file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read_indexhoppingcounts(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Index_Hopping_Counts.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read_topunknownbarcodes"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read_topunknownbarcodes}{}}}
+\subsection{Method \code{read_topunknownbarcodes()}}{
+Read Top_Unknown_Barcodes.csv file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read_topunknownbarcodes(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to Top_Unknown_Barcodes.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read_fastqlist"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read_fastqlist}{}}}
+\subsection{Method \code{read_fastqlist()}}{
+Read fastq_list.csv file.
+\itemize{
+\item rgid: read group.
+\item rgsm: sample ID.
+\item rglb: library.
+\item lane: flow cell lane.
+\item readnum: read number (1 or 2).
+\item filepath: path to the FASTQ file.
+}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read_fastqlist(x)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{(\code{character(1)})\cr
+Path to fastq_list.csv file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-read"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-read}{}}}
+\subsection{Method \code{read()}}{
+Reads contents of \code{Reports} directory output by BCLConvert.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$read()}\if{html}{\out{</div>}}
+}
+
+\subsection{Returns}{
+A list of tibbles.
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-write"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-write}{}}}
+\subsection{Method \code{write()}}{
+Writes tidied contents of \code{Reports} directory output by BCLConvert.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$write(
+  d,
+  out_dir = NULL,
+  prefix,
+  out_format = "tsv",
+  drid = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{d}}{Parsed object from \code{self$read()}.}
+
+\item{\code{out_dir}}{Output directory.}
+
+\item{\code{prefix}}{Prefix of output file(s).}
+
+\item{\code{out_format}}{Format of output file(s).}
+
+\item{\code{drid}}{dracarys ID to use for the dataset (e.g. \code{wfrid.123}, \code{prid.456}).}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-BclconvertReports375-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-BclconvertReports375-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{BclconvertReports375$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/man/Wf_bcl_convert.Rd b/man/Wf_bcl_convert.Rd
deleted file mode 100644
index 60256be..0000000
--- a/man/Wf_bcl_convert.Rd
+++ /dev/null
@@ -1,86 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bclconvert.R
-\name{Wf_bcl_convert}
-\alias{Wf_bcl_convert}
-\title{bcl_convert Wf R6 Class}
-\description{
-Contains methods for reading and processing files output from the UMCCR
-\code{bcl_convert} workflow.
-}
-\examples{
-\dontrun{
-indir <- file.path()
-sample_id <- "PTC_ctTSO240429"
-library_id <- "L2400482"
-d <- TsoCombinedVariantOutputFile$new(x)
-d$read()
-}
-}
-\section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{indir}}{Input directory containing Reports per assay type
-(e.g. /primary_data/240607_A01052_0209_BHLHFTDSXC/2024061140802544/).}
-}
-\if{html}{\out{</div>}}
-}
-\section{Methods}{
-\subsection{Public methods}{
-\itemize{
-\item \href{#method-Wf_bcl_convert-new}{\code{Wf_bcl_convert$new()}}
-\item \href{#method-Wf_bcl_convert-print}{\code{Wf_bcl_convert$print()}}
-\item \href{#method-Wf_bcl_convert-clone}{\code{Wf_bcl_convert$clone()}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-Wf_bcl_convert-new"></a>}}
-\if{latex}{\out{\hypertarget{method-Wf_bcl_convert-new}{}}}
-\subsection{Method \code{new()}}{
-Create a new Wf_bcl_convert object.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{Wf_bcl_convert$new(indir)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{indir}}{Input directory containing Reports per assay type.}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-Wf_bcl_convert-print"></a>}}
-\if{latex}{\out{\hypertarget{method-Wf_bcl_convert-print}{}}}
-\subsection{Method \code{print()}}{
-Print details about the Workflow
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{Wf_bcl_convert$print(...)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{...}}{(ignored).}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-Wf_bcl_convert-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-Wf_bcl_convert-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{Wf_bcl_convert$clone(deep = FALSE)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{</div>}}
-}
-}
-}
diff --git a/man/Wf_tso_ctdna_tumor_only.Rd b/man/Wf_tso_ctdna_tumor_only.Rd
index 81c2baa..0af943d 100644
--- a/man/Wf_tso_ctdna_tumor_only.Rd
+++ b/man/Wf_tso_ctdna_tumor_only.Rd
@@ -12,7 +12,7 @@ Contains methods for reading and processing files output from the UMCCR
 x <- file.path(
   "~/icav1/g/production/analysis_data/SBJ00596/tso_ctdna_tumor_only",
   "2024050555972acf/L2400482/Results/PTC_ctTSO240429_L2400482/dracarys_gds_sync"
-  )
+)
 sample_id <- "PTC_ctTSO240429"
 library_id <- "L2400482"
 d <- TsoCombinedVariantOutputFile$new(x)