diff --git a/R/meta_rnasum.R b/R/meta_rnasum.R
index 7c4febb..08e36c8 100644
--- a/R/meta_rnasum.R
+++ b/R/meta_rnasum.R
@@ -28,12 +28,30 @@ meta_rnasum <- function(pmeta, status = "Succeeded") {
     meta_io_fromjson() |>
     dplyr::mutate(
       # input
+      # renamed in v1.1.0
       gds_indir_dragen = purrr::map_chr(.data$input, list("dragen_transcriptome_directory", "location"), .default = NA),
+      gds_indir_dragen = ifelse(
+        is.na(gds_indir_dragen),
+        purrr::map_chr(.data$input, list("dragen_wts_dir", "location"), .default = NA),
+        gds_indir_dragen
+      ),
       gds_indir_umccrise = purrr::map_chr(.data$input, list("umccrise_directory", "location"), .default = NA),
+      # renamed in v1.1.0
       gds_indir_arriba = purrr::map_chr(.data$input, list("arriba_directory", "location"), .default = NA),
+      gds_indir_arriba = ifelse(
+        is.na(gds_indir_arriba),
+        purrr::map_chr(.data$input, list("arriba_dir", "location"), .default = NA),
+        gds_indir_arriba
+      ),
       rnasum_sample_name = purrr::map_chr(.data$input, "sample_name", .default = NA),
       rnasum_dataset = purrr::map_chr(.data$input, "dataset", .default = NA),
       rnasum_report_dir = purrr::map_chr(.data$input, "report_directory", .default = NA),
+      # renamed in v1.1.0
+      rnasum_report_dir = ifelse(
+        is.na(rnasum_report_dir),
+        purrr::map_chr(.data$input, "report_dir", .default = NA),
+        rnasum_report_dir
+      ),
       sbjid1 = sub("(SBJ.*)__L.*", "\\1", .data$rnasum_report_dir),
       libid1 = sub("(SBJ.*)__(L.*)", "\\2", .data$rnasum_report_dir),
       # output
diff --git a/R/meta_wgs_alignment_qc.R b/R/meta_wgs_alignment_qc.R
index 3d4b6f4..70284f0 100644
--- a/R/meta_wgs_alignment_qc.R
+++ b/R/meta_wgs_alignment_qc.R
@@ -10,7 +10,7 @@
 #'   readr::read_rds()
 #' (m <- meta_wgs_alignment_qc(pmeta))
 #' @testexamples
-#' expect_equal("Lane" %in% colnames(m), TRUE)
+#' expect_equal("lane" %in% colnames(m), TRUE)
 #' @export
 meta_wgs_alignment_qc <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status
@@ -27,22 +27,36 @@ meta_wgs_alignment_qc <- function(pmeta, status = "Succeeded") {
     meta_io_fromjson() |>
     dplyr::mutate(
       # input
-      rglb = purrr::map_chr(.data$input, list("fastq_list_rows", "rglb")),
+      rgid = purrr::map_chr(.data$input, list("fastq_list_rows", "rgid")),
       rgsm = purrr::map_chr(.data$input, list("fastq_list_rows", "rgsm")),
+      rglb = purrr::map_chr(.data$input, list("fastq_list_rows", "rglb")),
       lane = purrr::map_int(.data$input, list("fastq_list_rows", "lane")),
       lane = as.character(.data$lane),
+      # read_1/read_2 are dfs
+      fq1 = purrr::map_chr(.data$input, list("fastq_list_rows", "read_1", "location"), .default = NA),
+      fq2 = purrr::map_chr(.data$input, list("fastq_list_rows", "read_2", "location"), .default = NA),
       # output
       gds_outdir_dragen = purrr::map_chr(.data$output, list("dragen_alignment_output_directory", "location"), .default = NA),
       gds_outdir_multiqc = purrr::map_chr(.data$output, list("multiqc_output_directory", "location"), .default = NA),
       SubjectID = sub("umccr__automated__wgs_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
+    ) |>
+    tidyr::separate_wider_delim(
+      cols = "rgid", delim = ".",
+      names = c("index1", "index2", "lane2", "illumina_id", "sample_lib_id")
     )
+
   d |>
     dplyr::select(
       dplyr::all_of(meta_main_cols()),
       "SubjectID",
       LibraryID = "rglb",
       SampleID = "rgsm",
-      Lane = "lane",
+      "lane",
+      "index1",
+      "index2",
+      "illumina_id",
+      "fq1",
+      "fq2",
       "gds_outdir_dragen",
       "gds_outdir_multiqc",
     )
diff --git a/R/meta_wts_alignment_qc.R b/R/meta_wts_alignment_qc.R
index ddba214..715f2fa 100644
--- a/R/meta_wts_alignment_qc.R
+++ b/R/meta_wts_alignment_qc.R
@@ -10,7 +10,7 @@
 #'   readr::read_rds()
 #' (m <- meta_wts_alignment_qc(pmeta))
 #' @testexamples
-#' expect_equal("Lane" %in% colnames(m), TRUE)
+#' expect_equal("lane" %in% colnames(m), TRUE)
 #' @export
 meta_wts_alignment_qc <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status
@@ -27,22 +27,36 @@ meta_wts_alignment_qc <- function(pmeta, status = "Succeeded") {
     meta_io_fromjson() |>
     dplyr::mutate(
       # input
-      rglb = purrr::map_chr(.data$input, list("fastq_list_rows", "rglb")),
+      rgid = purrr::map_chr(.data$input, list("fastq_list_rows", "rgid")),
       rgsm = purrr::map_chr(.data$input, list("fastq_list_rows", "rgsm")),
+      rglb = purrr::map_chr(.data$input, list("fastq_list_rows", "rglb")),
       lane = purrr::map_int(.data$input, list("fastq_list_rows", "lane")),
       lane = as.character(.data$lane),
+      # read_1/read_2 are dfs
+      fq1 = purrr::map_chr(.data$input, list("fastq_list_rows", "read_1", "location"), .default = NA),
+      fq2 = purrr::map_chr(.data$input, list("fastq_list_rows", "read_2", "location"), .default = NA),
       # output
       gds_outdir_dragen = purrr::map_chr(.data$output, list("dragen_alignment_output_directory", "location"), .default = NA),
       gds_outdir_multiqc = purrr::map_chr(.data$output, list("multiqc_output_directory", "location"), .default = NA),
       SubjectID = sub("umccr__automated__wts_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
+    ) |>
+    tidyr::separate_wider_delim(
+      cols = "rgid", delim = ".",
+      names = c("index1", "index2", "lane2", "illumina_id", "sample_lib_id")
     )
+
   d |>
     dplyr::select(
       dplyr::all_of(meta_main_cols()),
       "SubjectID",
       LibraryID = "rglb",
       SampleID = "rgsm",
-      Lane = "lane",
+      "lane",
+      "index1",
+      "index2",
+      "illumina_id",
+      "fq1",
+      "fq2",
       "gds_outdir_dragen",
       "gds_outdir_multiqc",
     )
diff --git a/inst/reports/seqrunsum/funcs.R b/inst/reports/seqrunsum/funcs.R
index f3f7886..2ebc3e1 100644
--- a/inst/reports/seqrunsum/funcs.R
+++ b/inst/reports/seqrunsum/funcs.R
@@ -1,4 +1,42 @@
 funcs <- list(
+  gds_fastqlistcsv_read = function(gdsdir, token, page_size = 20) {
+    .read_fastqlist <- function(x) {
+      nms <- tibble::tribble(
+        ~new_nm, ~old_nm, ~class,
+        "rgid", "RGID", "c",
+        "SampleID_LibraryID", "RGSM", "c",
+        "rglb", "RGLB", "c",
+        "lane", "Lane", "c",
+        "1", "Read1File", "c",
+        "2", "Read2File", "c"
+      )
+      lookup <- tibble::deframe(nms[c("new_nm", "old_nm")])
+      d <- readr::read_csv(x, col_types = readr::cols(.default = "c"))
+      assertthat::assert_that(all(colnames(d) == nms[["old_nm"]]))
+      d |>
+        dplyr::rename(dplyr::all_of(lookup)) |>
+        dplyr::mutate(
+          SampleID = sub("(.*)_(L.*)", "\\1", .data$SampleID_LibraryID),
+          LibraryID = sub("(.*)_(L.*)", "\\2", .data$SampleID_LibraryID),
+          topup = grepl("topup", .data$LibraryID)
+        ) |>
+        dplyr::select("rgid", "SampleID", "LibraryID", "lane", "1", "2", "topup") |>
+        tidyr::pivot_longer(c("1", "2"), names_to = "read", values_to = "path")
+    }
+    regex <- tibble::tribble(
+      ~regex, ~fun,
+      "fastq_list\\.csv$", "fastq_list"
+    )
+    g <- dracarys::gds_files_list_filter_relevant(
+      gdsdir = gdsdir, token = token, pattern = NULL, include_url = TRUE,
+      page_size = page_size, regexes = regex
+    )
+    assertthat::assert_that(
+      nrow(g) == 1,
+      all(colnames(g) == c("type", "bname", "size", "file_id", "path", "presigned_url"))
+    )
+    .read_fastqlist(g$presigned_url)
+  },
   #----#
   kable_empty_wf = function(wf) {
     kableExtra::kbl(NULL, caption = glue("<strong>NO {wf} WORKFLOWS WERE RUN</strong>"), escape = FALSE) |>
@@ -49,10 +87,10 @@ funcs <- list(
       ) |>
       ungroup() |>
       tidyr::unnest(clrs) |>
+      distinct(.data$clrs, .keep_all = TRUE) |>
       pull(clrs)
-    max_col <- length(clrs)
-    stopifnot(nc <= max_col, nc > 0)
-    clrs[seq_len(nc)]
+    # recycle colour vector according to nc
+    rep_len(clrs, length.out = nc)
   },
   #----#
   get_sbj_url = function(x, colour = NULL, account = "pro") {
diff --git a/inst/reports/seqrunsum/render.sh b/inst/reports/seqrunsum/render.sh
index 94f3f55..25b00da 100644
--- a/inst/reports/seqrunsum/render.sh
+++ b/inst/reports/seqrunsum/render.sh
@@ -1,9 +1,9 @@
-start="2024-05-18"
-end="2024-05-20"
-out="seqrunsum_${start}_${end}.html"
+date_start="2024-08-03"
+date_end="2024-08-05"
+out="seqrunsum_${date_start}_${date_end}.html"
 
 quarto render report.qmd \
-    -P date_start:${start} \
-    -P date_end:${end} \
+    -P date_start:${date_start} \
+    -P date_end:${date_end} \
     -o ${out} \
     --output-dir nogit
diff --git a/inst/reports/seqrunsum/report.qmd b/inst/reports/seqrunsum/report.qmd
index 856e5a0..1092eb5 100644
--- a/inst/reports/seqrunsum/report.qmd
+++ b/inst/reports/seqrunsum/report.qmd
@@ -1,6 +1,6 @@
 ---
 title: "{{< meta params.title >}}"
-subtitle: "Period: {{< meta params.date_start >}} to {{< meta params.date_end >}}"
+subtitle: "Period: `r paste(params$date_start, ' to ', params$date_end)`"
 author: "UMCCR - Genomics Platform Group"
 date: now
 date-format: "YYYY-MM-DD HH:mm Z"
@@ -27,8 +27,8 @@ format:
       body-width: 1300px
 params:
   title: "UMCCR PortalDB Workflow Summary"
-  date_start: "2024-06-15"
-  date_end: "2024-06-17"
+  date_start: "XXXX-XX-XX"
+  date_end: "XXXX-XX-XX"
 ---
 
 ```{r}
@@ -55,6 +55,17 @@ params:
 set.seed(42)
 ```
 
+```{r}
+#| label: aws_connect
+invisible(capture.output(rportal::awsvault_profile("upro")))
+```
+
+```{r}
+#| label: ica_token
+# required for directly parsing fastq_list.csv and listing FASTQs on GDS
+ica_token <- Sys.getenv("ICA_ACCESS_TOKEN")
+```
+
 ```{r funcs_source}
 source(here("inst/reports/seqrunsum/funcs.R"))
 ```
@@ -87,13 +98,9 @@ wfs <- tibble::tribble(
 
 ```{r}
 #| label: query_workflow_table
-invisible(capture.output(rportal::awsvault_profile("upro")))
+#| message: false
 query_wf <- glue('WHERE "start" >= date(\'{dstart}\') AND "start" <= date(\'{dend}\') ORDER BY "start" DESC;')
-pmeta_rds <- here(glue("nogit/data_portal/workflows/{as.Date(date_end)}.rds"))
-# fs::dir_create(here(glue("nogit/data_portal/workflows")))
-# pmeta_raw <- rportal::portaldb_query_workflow(query_wf)
-# saveRDS(pmeta_raw, file = pmeta_rds)
-pmeta_raw <- readr::read_rds(pmeta_rds)
+pmeta_raw <- rportal::portaldb_query_workflow(query_wf)
 # check there are no rogue unaccounted wfs run
 stopifnot(all(pmeta_raw[["type_name"]] %in% wfs[["name"]]))
 ```
@@ -120,21 +127,21 @@ sbjids <- funcs$get_ids(pmeta_tidy, "SubjectID") # not used anywhere (yet?)
 
 ```{r}
 #| label: query_limsrow_table
-# fs::dir_create(here(glue("nogit/data_portal/lims")))
-lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds"))
+#| message: false
 libidsq <- paste(libids, collapse = "|")
 query_lims <- glue("WHERE REGEXP_LIKE(\"library_id\", '{libidsq}');")
-# lims_raw <- rportal::portaldb_query_limsrow(query_lims)
-# saveRDS(lims_raw, file = lims_rds)
-lims_raw <- readr::read_rds(lims_rds)
+lims_raw <- rportal::portaldb_query_limsrow(query_lims)
 lims <- lims_raw |>
   select(
     SubjectID = "subject_id", SampleID = "sample_id", LibraryID = "library_id",
     ExternalSubjectID = "external_subject_id",
     ProjectOwner = "project_owner", ProjectName = "project_name",
-    Type = "type", Assay = "assay", Phenotype = "phenotype",
-    Source = "source", Quality = "quality", Topup = "topup", Workflow = "workflow"
-  )
+    Type = "type",
+    Phenotype = "phenotype",
+    Topup = "topup", Workflow = "workflow",
+    Assay = "assay", Source = "source",
+  ) |>
+  distinct()
 ```
 
 ```{r}
@@ -196,6 +203,73 @@ funcs$sbj_wf_count_tbl(pmeta_sumy)
 funcs$plot_vistime(pmeta_sumy)
 ```
 
+## FASTQ Summary
+
+Check FASTQs generated via the `bcl_convert` workflows.
+
+```{r}
+SubjectID_def <- reactable::colDef(html = TRUE, minWidth = 120)
+wf <- "bcl_convert"
+if (!chunks1[[wf]]) {
+  funcs$kable_empty_wf(wf)
+}
+```
+
+```{r eval=chunks1[[wf]]}
+#| label: fastq_summary
+
+# first list FASTQs in the bcl_convert output directories
+gds_outdirs_fastq <- pmeta_tidy[[wf]] |>
+  select("gds_outdirs_fastq") |>
+  tidyr::unnest("gds_outdirs_fastq") |>
+  distinct() |>
+  mutate(outdirs_reports = file.path(.data$gds_outdirs_fastq, "Reports"))
+gds_fastqs1 <- gds_outdirs_fastq |>
+  select("gds_outdirs_fastq") |>
+  rowwise() |>
+  mutate(
+    list_fqs = list(
+      dracarys::gds_files_list_fastq(
+        gdsdir = .data$gds_outdirs_fastq, token = ica_token, page_size = 200
+      )
+    )
+  ) |>
+  ungroup() |>
+  tidyr::unnest("list_fqs") |>
+  select("path", "size", "size_chr", "size_num")
+# now grab the Reports/fastq_list.csv files to check consistency
+# across listed FASTQs and found FASTQs
+gds_fastqs2 <- gds_outdirs_fastq |>
+  rowwise() |>
+  mutate(fq = list(funcs$gds_fastqlistcsv_read(.data$outdirs_reports, token = ica_token, page_size = 20))) |>
+  ungroup() |>
+  tidyr::unnest("fq") |>
+  mutate(path = file.path(dirname(.data$gds_outdirs_fastq), .data$path)) |>
+  select("LibraryID", "SampleID", "path", "topup", "read", "lane", "rgid")
+
+stopifnot(nrow(gds_fastqs1) == nrow(gds_fastqs2))
+stopifnot(all(gds_fastqs1$path %in% gds_fastqs2$path))
+# now join to get the file sizes
+fq <- gds_fastqs2 |>
+  left_join(gds_fastqs1, by = "path") |>
+  select("LibraryID", "SampleID", "path", "size_num", "size_chr", "topup", "rgid", "read", "lane") |>
+  left_join(
+    lims |>
+      select("SubjectID", "SampleID", "LibraryID", "Type", "Phenotype", "Workflow", "Assay") |>
+      distinct(),
+    by = c("LibraryID", "SampleID")
+  ) |>
+  select(
+    "SubjectID", "LibraryID", "SampleID", "size_num", "size_chr", "Type", "Phenotype",
+    "Workflow", "Assay", "path", "topup", "rgid", "read", "lane", everything()
+  ) |>
+  left_join(clrs1 |> select("sbjid", "sbj_url"), by = c("SubjectID" = "sbjid")) |>
+  mutate(SubjectID = if_else(is.na(.data$sbj_url), funcs$get_sbj_url(.data$SubjectID), .data$sbj_url)) |>
+  arrange(desc(SubjectID))
+
+funcs$dt_view(fq, id = "FASTQs", columns = list(SubjectID = SubjectID_def))
+```
+
 ## Workflow Metadata
 
 ```{r}
@@ -211,13 +285,11 @@ end_status_def <- reactable::colDef(
     list(color = color, fontweight = "bold")
   }
 )
-SubjectID_def <- reactable::colDef(html = TRUE, minWidth = 120)
 ```
 
 ::: {.panel-tabset .nav-pills}
 
 ```{r}
-#| echo: false
 wf <- "bcl_convert"
 ```
 
@@ -243,7 +315,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "portal_run_id", "durationMin", "runfolder_name", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "batch_name", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "batch_name", "Type", "Assay", "Source", "Workflow",
     "start", "end", contains("gds_outdir")
   ) |>
   arrange(portal_run_id, desc(SubjectID), start) |>
@@ -272,7 +344,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -280,7 +352,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "wgs_alignment_qc"
 ```
 
@@ -301,8 +372,8 @@ pmeta_tidy[[wf]] |>
     durationMin = round(as.numeric(difftime(end, start, units = "mins")))
   ) |>
   select(
-    "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "Lane", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "lane", "ExternalSubjectID",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_dragen"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -310,7 +381,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "wts_alignment_qc"
 ```
 
@@ -331,8 +401,8 @@ pmeta_tidy[[wf]] |>
     durationMin = round(as.numeric(difftime(end, start, units = "mins")))
   ) |>
   select(
-    "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "Lane", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "lane", "ExternalSubjectID",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_dragen"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -340,7 +410,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "wts_tumor_only"
 ```
 
@@ -362,7 +431,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID", "ProjectOwner", "ProjectName",
-    "Type", "Assay", "Source", "Quality", "Workflow",
+    "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_dragen"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -370,7 +439,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "wgs_tumor_normal"
 ```
 
@@ -397,7 +465,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID", "ProjectOwner", "ProjectName",
-    "Type", "Assay", "Source", "Quality", "Workflow",
+    "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_dragen_somatic", "gds_outdir_dragen_germline"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -405,7 +473,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "umccrise"
 ```
 
@@ -432,7 +499,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_umccrise"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -440,7 +507,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "rnasum"
 ```
 
@@ -462,7 +528,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "rnasum_dataset", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "gds_outdir_rnasum",
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -470,7 +536,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "star_alignment"
 ```
 
@@ -492,7 +557,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID", "ProjectOwner", "ProjectName",
-    "Type", "Assay", "Source", "Quality", "Workflow",
+    "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "s3_outdir_star"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -500,7 +565,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "oncoanalyser_wts"
 ```
 
@@ -522,7 +586,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID", "ProjectOwner", "ProjectName",
-    "Type", "Assay", "Source", "Quality", "Workflow",
+    "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "s3_outdir_oncoanalyser"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -531,7 +595,6 @@ pmeta_tidy[[wf]] |>
 
 
 ```{r}
-#| echo: false
 wf <- "oncoanalyser_wgs"
 ```
 
@@ -558,7 +621,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "s3_outdir_oncoanalyser"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -566,7 +629,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "oncoanalyser_wgts_existing_both"
 ```
 
@@ -594,7 +656,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "WGTS", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "s3_outdir_oncoanalyser"
   ) |>
   arrange(desc(SubjectID), start) |>
@@ -602,7 +664,6 @@ pmeta_tidy[[wf]] |>
 ```
 
 ```{r}
-#| echo: false
 wf <- "sash"
 ```
 
@@ -629,7 +690,7 @@ pmeta_tidy[[wf]] |>
   ) |>
   select(
     "end_status", "durationMin", "SubjectID", "LibraryID", "SampleID", "Phenotype", "ExternalSubjectID",
-    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Quality", "Workflow",
+    "ProjectOwner", "ProjectName", "Type", "Assay", "Source", "Workflow",
     "portal_run_id", "wfr_id", "start", "end", "s3_outdir_sash"
   ) |>
   arrange(desc(SubjectID), start) |>
diff --git a/man/portaldb_query_limsrow.Rd b/man/portaldb_query_limsrow.Rd
index 1fcf1cc..cba3c96 100644
--- a/man/portaldb_query_limsrow.Rd
+++ b/man/portaldb_query_limsrow.Rd
@@ -25,8 +25,10 @@ libids <- shQuote(paste(c("L2400340", "L2400256"), collapse = "|"))
 query1 <- glue("WHERE REGEXP_LIKE(\"library_id\", {libids});")
 portaldb_query_limsrow(query1)
 sbjids <- paste(c("SBJ04470", "SBJ04487", "SBJ04488"), collapse = "|")
-query2 <- glue("WHERE REGEXP_LIKE(\"subject_id\", '{sbjids}') AND \"type\" = 'WGS' ",
-               "AND \"phenotype\" = 'tumor' ORDER BY \"subject_id\" DESC;")
+query2 <- glue(
+  "WHERE REGEXP_LIKE(\"subject_id\", '{sbjids}') AND \"type\" = 'WGS' ",
+  "AND \"phenotype\" = 'tumor' ORDER BY \"subject_id\" DESC;"
+)
 d <- portaldb_query_limsrow(query2)
 # get tumor libids for each sbjid
 d |> dplyr::select(subject_id, library_id)
diff --git a/tests/testthat/test-roxytest-testexamples-meta_wgs_alignment_qc.R b/tests/testthat/test-roxytest-testexamples-meta_wgs_alignment_qc.R
index bfe4769..e00898b 100644
--- a/tests/testthat/test-roxytest-testexamples-meta_wgs_alignment_qc.R
+++ b/tests/testthat/test-roxytest-testexamples-meta_wgs_alignment_qc.R
@@ -8,6 +8,6 @@ test_that("Function meta_wgs_alignment_qc() @ L15", {
     system.file(package = "rportal") |>
     readr::read_rds()
   (m <- meta_wgs_alignment_qc(pmeta))
-  expect_equal("Lane" %in% colnames(m), TRUE)
+  expect_equal("lane" %in% colnames(m), TRUE)
 })
 
diff --git a/tests/testthat/test-roxytest-testexamples-meta_wts_alignment_qc.R b/tests/testthat/test-roxytest-testexamples-meta_wts_alignment_qc.R
index 7434438..f0a01ad 100644
--- a/tests/testthat/test-roxytest-testexamples-meta_wts_alignment_qc.R
+++ b/tests/testthat/test-roxytest-testexamples-meta_wts_alignment_qc.R
@@ -8,6 +8,6 @@ test_that("Function meta_wts_alignment_qc() @ L15", {
     system.file(package = "rportal") |>
     readr::read_rds()
   (m <- meta_wts_alignment_qc(pmeta))
-  expect_equal("Lane" %in% colnames(m), TRUE)
+  expect_equal("lane" %in% colnames(m), TRUE)
 })