Create a combined annotation table per sample and per reference.

workflow/Snakefile

@@ -554,6 +554,44 @@ def get_output4cell_type_annotation() -> list[str]:
         for k in NORMALISATION_ID
         for m in filenames
     ]
+
+def get_combined_label_outputs() -> list[str]:
+    prefix: str = f'{config["output_path"]}/cell_type_annotation'
+
+    samples_by_conditions: dict[str, list[str]] = get_dict_value(
+        config,
+        "experiments",
+        cc.EXPERIMENTS_COLLECTIONS_NAME,
+        cc.EXPERIMENTS_COLLECTIONS_CONDITIONS_NAME,
+    )
+
+    annotations_by_conditions: dict[str, list[str]] = get_dict_value(
+        config,
+        cc.WILDCARDS_NAME,
+        cc.WILDCARDS_CELL_TYPE_ANNOTATION_NAME,
+    )
+
+    samples_annotations: list[tuple[str, str]] = cross_values_by_key(
+        samples_by_conditions,
+        annotations_by_conditions,
+    )
+
+    return [
+        os.path.join(
+            prefix,
+            seg,
+            sample,
+            norm,
+            annotation.split("/")[0],          # approach (e.g. reference_based)
+            annotation.split("/")[1],          # reference_name
+            "combined_labels.parquet",
+        )
+        for seg in SEGMENTATION_ID
+        for (sample, annotation) in samples_annotations
+        for norm in NORMALISATION_ID
+    ]
+
+
 
 
 def get_output4joint_analysis() -> list[str] | None:
@@ -1319,13 +1357,14 @@ def get_input2all(
 
     if cell_type_annotation:
         ret.extend(get_output4cell_type_annotation())
+        ret.extend(get_combined_label_outputs()) 
 
         if neighborhood_analysis:
             ret.extend(get_output4neighborhood_analysis())
 
         if doublet_finding:
             ret.extend(get_output4doublet_finding())
-        
+
     if count_correction:
         ret.extend(get_output4count_correction(
             cell_type_annotation,

workflow/rules/_cell_type_annotation/combine_annotation_results.smk

@@ -0,0 +1,30 @@
+#######################################
+#                Rules                #
+#######################################
+
+rule combineAnnotationLabels:
+    wildcard_constraints:
+        reference_name="[^/]+"
+
+    input:
+      root_dir=lambda wc: os.path.join(
+            config["output_path"],
+            "cell_type_annotation",
+            wc.segmentation_id,
+            wc.sample_id,
+            wc.normalisation_id,
+            "reference_based",
+            wc.reference_name
+        )
+
+    output:
+        combined=f'{config["output_path"]}/cell_type_annotation/{{segmentation_id}}/{{sample_id}}/{{normalisation_id}}/reference_based/{{reference_name}}/combined_labels.parquet'
+
+    log:
+        f'{config["output_path"]}/cell_type_annotation/{{segmentation_id}}/{{sample_id}}/{{normalisation_id}}/reference_based/{{reference_name}}/logs/combineAnnotationLabels.log'
+    container:
+        config["containers"]["r"]
+    threads: 1
+    script:
+        "../../scripts/_cell_type_annotation/combine_annotation_results.R"
+

workflow/rules/cell_type_annotation.smk

@@ -135,3 +135,5 @@ include: "_cell_type_annotation/_reference_based/rctd.smk"
 include: "_cell_type_annotation/_reference_based/singler.smk"
 include: "_cell_type_annotation/_reference_based/seurat.smk"
 include: "_cell_type_annotation/_reference_based/xgboost.smk"
+
+include: "_cell_type_annotation/combine_annotation_results.smk"

workflow/scripts/_cell_type_annotation/combine_annotation_results.R

@@ -0,0 +1,51 @@
+log <- file(snakemake@log[[1]], open = "wt")
+sink(log, type = "output")
+sink(log, type = "message")
+
+library(dplyr)
+library(arrow)
+library(stringr)
+library(purrr)
+
+input_dir <- snakemake@input[["root_dir"]]
+
+# Find all labels.parquet files under input_dir
+label_files <- list.files(
+  path = input_dir,
+  pattern = "^labels\\.parquet$",
+  full.names = TRUE,
+  recursive = TRUE
+)
+
+if (length(label_files) == 0) {
+  stop("No labels.parquet files found under: ", input_dir)
+}
+
+
+read_and_annotate <- function(path) {
+  df <- read_parquet(path)
+
+  # Extract tool/level/mode from path
+  parts <- str_split(path, .Platform$file.sep)[[1]]
+  n <- length(parts)
+
+  if (n < 4) {
+    stop("Unexpected path structure (too few components): ", path)
+  }
+
+  mode <- parts[n - 1]
+  level <- parts[n - 2]
+  tool  <- parts[n - 3]
+
+  prefix <- paste(level, tool, mode, sep = "/")
+
+  # Rename columns except cell_id
+  colnames(df)[colnames(df) != "cell_id"] <- paste0(prefix, "/", colnames(df)[colnames(df) != "cell_id"])
+  return(df)
+}
+
+merged <- label_files %>%
+  map(read_and_annotate) %>%
+  reduce(full_join, by = "cell_id")
+
+write_parquet(merged, snakemake@output[["combined"]])