diff --git a/pipeline-runner/R/qc-7-embed_and_cluster.R b/pipeline-runner/R/qc-7-embed_and_cluster.R
index baf04c37..f8afe999 100644
--- a/pipeline-runner/R/qc-7-embed_and_cluster.R
+++ b/pipeline-runner/R/qc-7-embed_and_cluster.R
@@ -221,8 +221,7 @@ make_cl_metadata_cellsets <- function(scdata, config) {
   cl_metadata <- download_cl_metadata_file(config)
 
   # TODO deduplicate using sample column (if present) in the cell-level metadata file
-  # TODO add "duplicated" variable to cl_metadata table to create cellset for duplicated barcodes
-  #cl_metadata <- deduplicate_cl_metadata(scdata, cl_metadata)
+  cl_metadata <- add_duplicate_barcode_column(cl_metadata)
 
   # extract barcode - cell_id (keep sample column for variable type detection)
   barcode_cell_id_map <- get_cell_id_barcode_map(scdata)
@@ -343,6 +342,8 @@ detect_variable_types <- function(cl_metadata) {
   # remove samples var, useless from this point on
   clm_cols <- grep("^samples$", clm_cols, value = T, invert = T)
 
+  clm_cols <- c(clm_cols, "duplicate_barcode")
+
   return(list(CLM = clm_cols, CLMPerSample = clm_per_sample_cols))
 }
 
@@ -373,13 +374,21 @@ make_cl_metadata_cellclass <- function(variable, type, cl_metadata, color_pool)
   values <- unique(cl_metadata[[variable]])
 
   for (i in seq_along(values)) {
+
+    cell_ids <- cl_metadata[get(variable) == values[i] & cl_metadata$duplicate_barcode == "no", cells_id]
+
+    # do not add duplicate barcodes, except for the duplicate_barcode cellset
+    if (variable == "duplicate_barcode") {
+      cell_ids <- cl_metadata[get(variable) == values[i], cells_id]
+    }
+
     cl_metadata_cellset$children[[i]] <- list(
       key = uuid::UUIDgenerate(),
       name = as.character(values[i]),
       rootNode = FALSE,
       type = type,
       color = color_pool[1],
-      cellIds = ensure_is_list_in_json(cl_metadata[get(variable) == values[i], cells_id])
+      cellIds = ensure_is_list_in_json(cell_ids)
     )
     color_pool <- color_pool[-1]
   }
@@ -442,3 +451,10 @@ sort_cluster_names <- function(strings) {
 
   return(strings[sorted_indices])
 }
+
+add_duplicate_barcode_column <- function(cl_metadata){
+  dup_barcodes <- vctrs::vec_duplicate_detect(cl_metadata$barcode)
+
+  cl_metadata$duplicate_barcode <- ifelse(dup_barcodes, "yes", "no")
+  return(cl_metadata)
+}
diff --git a/pipeline-runner/tests/testthat/test-qc-7-embed_and_cluster.R b/pipeline-runner/tests/testthat/test-qc-7-embed_and_cluster.R
index 32d5d303..aa2dd10c 100644
--- a/pipeline-runner/tests/testthat/test-qc-7-embed_and_cluster.R
+++ b/pipeline-runner/tests/testthat/test-qc-7-embed_and_cluster.R
@@ -476,7 +476,7 @@ test_that("detect_variable_types correctly detects variable types", {
 
   expected_var_types <-
     list(
-      CLM = c("cell_type"),
+      CLM = c("cell_type", "duplicate_barcode"),
       CLMPerSample = c("group_var", "redundant_group_var")
     )
 
@@ -590,10 +590,11 @@ test_that("make_cl_metadata_cellsets makes cell-level metadata cellsets.", {
   res <- stubbed_make_cl_metadata_cellsets(scdata, config)
   withr::defer(unlink(file.path(".", basename(config$metadataS3Path))))
 
-  expect_equal(length(res), 3)
+  expect_equal(length(res), 4)
   expect_equal(length(res[[1]]$children), length(unique(cl_metadata$cell_type)))
-  expect_equal(length(res[[2]]$children), length(unique(cl_metadata$group_var)))
-  expect_equal(length(res[[3]]$children), length(unique(cl_metadata$redundant_group_var)))
+  expect_equal(length(res[[2]]$children), 1)
+  expect_equal(length(res[[3]]$children), length(unique(cl_metadata$group_var)))
+  expect_equal(length(res[[4]]$children), length(unique(cl_metadata$redundant_group_var)))
 
   cell_class_names <- c("key", "name", "rootNode", "type", "children")
   purrr::walk(res, expect_named, cell_class_names)
@@ -618,3 +619,88 @@ with_fake_http(
     )
   })
 )
+
+test_that("make_cl_metadata_table works with duplicate barcodes", {
+  config <- mock_config()
+  scdata <- mock_scdata()
+  cl_metadata <- mock_cl_metadata(scdata)
+  cl_metadata <- rbind(cl_metadata, cl_metadata[1:2,])
+
+  local_mock_cl_metadata_table(cl_metadata, "mock_experiment_id")
+
+  res <- stubbed_make_cl_metadata_cellsets(scdata, config)
+  withr::defer(unlink(file.path(".", basename(config$metadataS3Path))))
+
+  expect_equal(length(res), 4)
+  expect_equal(length(res[[1]]$children), length(unique(cl_metadata$cell_type)))
+  expect_equal(length(res[[2]]$children), 2)
+  expect_equal(length(res[[3]]$children), length(unique(cl_metadata$group_var)))
+  expect_equal(length(res[[4]]$children), length(unique(cl_metadata$redundant_group_var)))
+
+  cell_class_names <- c("key", "name", "rootNode", "type", "children")
+  purrr::walk(res, expect_named, cell_class_names)
+
+  # cellsets have the same keys as cell classes except children, color and cellIds
+  for (i in seq_along(res)) {
+    purrr::walk(res[[i]]$children, expect_named, c(cell_class_names[-5], "color", "cellIds"))
+  }
+})
+
+test_that("add_duplicate_barcode_column handles empty input correctly", {
+  empty_cl_metadata <- data.frame(barcode = character(0))
+  expect_equal(nrow(add_duplicate_barcode_column(empty_cl_metadata)), 0)
+})
+
+test_that("add_duplicate_barcode_column handles unique barcodes correctly", {
+  unique_cl_metadata <- data.frame(barcode = c("BC01", "BC02", "BC03"))
+  unique_result <- add_duplicate_barcode_column(unique_cl_metadata)
+  expect_equal(unique_result$duplicate_barcode, c("no", "no", "no"))
+})
+
+test_that("add_duplicate_barcode_column handles duplicate barcodes correctly", {
+  dup_cl_metadata <- data.frame(barcode = c("BC01", "BC01", "BC02"))
+  dup_result <- add_duplicate_barcode_column(dup_cl_metadata)
+  expect_equal(dup_result$duplicate_barcode, c("yes", "yes", "no"))
+})
+
+test_that("add_duplicate_barcode_column handles a mix of unique and duplicate barcodes correctly", {
+  mixed_cl_metadata <- data.frame(barcode = c("BC01", "BC02", "BC02", "BC03"))
+  mixed_result <- add_duplicate_barcode_column(mixed_cl_metadata)
+  expect_equal(mixed_result$duplicate_barcode, c("no", "yes", "yes", "no"))
+})
+
+test_that("duplicate barcodes are not present in the created cellsets", {
+  config <- mock_config()
+  scdata <- mock_scdata()
+  cl_metadata <- mock_cl_metadata(scdata)
+  cl_metadata <- rbind(cl_metadata, cl_metadata[1:2, ])
+
+  cl_metadata_res <- add_duplicate_barcode_column(cl_metadata)
+  barcode_cell_id_map <- get_cell_id_barcode_map(scdata)
+  cl_metadata_table <-
+    make_cl_metadata_table(cl_metadata_res, barcode_cell_id_map)
+
+  local_mock_cl_metadata_table(cl_metadata, "mock_experiment_id")
+
+  res <- stubbed_make_cl_metadata_cellsets(scdata, config)
+  withr::defer(unlink(file.path(".", basename(config$metadataS3Path))))
+
+  dup_barcodes <- unique(cl_metadata_table[duplicate_barcode == "yes", cells_id])
+
+  for (item in res) {
+    if (item$name != "duplicate_barcode") {
+      for (child in item$children) {
+        has_duplicate_barcodes <- any(child$cellIds %in% dup_barcodes)
+        expect_false(has_duplicate_barcodes,
+          info = paste(
+            "Duplicate barcodes detected in", item$name,
+            "-", child$name
+          )
+        )
+      }
+    }
+  }
+})
+
+
+