Add cellassign organs to metadata

bin/add_celltypes_to_sce.R

@@ -42,6 +42,12 @@ option_list <- list(
     type = "character",
     help = "Name of marker by cell type reference file used with CellAssign.
             File name is expected to be in form: `<ref_name>_<source>_<version>.tsv`"
+  ),
+  make_option(
+    opt_str = c("--celltype_ref_metafile"),
+    type = "character",
+    help = "Metadata TSV file containing cell type reference metadata.
+            This file is used to obtain a list of organs used for CellAssign annotation."
   )
 )
 
@@ -177,6 +183,10 @@ if (!is.null(opt$cellassign_predictions)) {
     stop("CellAssign reference filename must be provided")
   }
 
+  if (is.null(opt$celltype_ref_metafile)) {
+    stop("Cell type reference metadata filename must be provided")
+  }
+
   predictions <- readr::read_tsv(opt$cellassign_predictions)
 
   # get cell type with maximum prediction value for each cell
@@ -216,6 +226,17 @@ if (!is.null(opt$cellassign_predictions)) {
   # note that if `metadata(sce)$celltype_methods` doesn't exist yet, this will
   #  come out to just the string "cellassign"
   metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "cellassign")
+
+  # add cellassign reference organs to metadata
+  cellassign_organs <- opt$celltype_ref_metafile |>
+    readr::read_tsv() |>
+    dplyr::filter(celltype_ref_name == cellassign_ref_info[["ref_name"]]) |>
+    dplyr::pull(organs)
+
+  if (cellassign_organs == "" | is.na(cellassign_organs)) {
+    stop("Failed to obtain CellAssign reference organ list.")
+  }
+  metadata(sce)$cellassign_reference_organs <- cellassign_organs
 }
 
 # export annotated object with cellassign assignments

main.nf

@@ -63,6 +63,18 @@ if (!resolution_strategies.contains(params.af_resolution)) {
   param_error = true
 }
 
+// cell type annotation file checks
+if (params.perform_celltyping) {
+  if (!file(params.project_celltype_metafile).exists()) {
+    log.error("The 'project_celltype_metafile' file '${params.project_celltype_metafile}' can not be found.")
+    param_error = true
+  }
+  if (!file(params.celltype_ref_metadata).exists()) {
+    log.error("The 'celltype_ref_metadata' file '${params.celltype_ref_metadata}' can not be found.")
+    param_error = true
+  }
+}
+
 if(param_error){
   System.exit(1)
 }

modules/classify-celltypes.nf

@@ -97,6 +97,7 @@ process add_celltypes_to_sce {
   tag "${meta.library_id}"
   input:
     tuple val(meta), path(processed_rds), path(singler_dir), path(cellassign_dir)
+    path(celltype_ref_metadata) // TSV file of references metadata needed for CellAssign only
   output:
     tuple val(meta), path(annotated_rds)
   script:
@@ -112,7 +113,8 @@ process add_celltypes_to_sce {
       ${singler_present ? "--singler_results  ${singler_results}" : ''} \
       ${singler_present ? "--singler_model_file ${meta.singler_model_file}" : ''} \
       ${cellassign_present ? "--cellassign_predictions  ${cellassign_predictions}" : ''} \
-      ${cellassign_present ? "--cellassign_ref_file ${meta.cellassign_reference_file}" : ''}
+      ${cellassign_present ? "--cellassign_ref_file ${meta.cellassign_reference_file}" : ''} \
+      ${cellassign_present ? "--celltype_ref_metafile ${celltype_ref_metadata}" : ''}
     """
   stub:
     annotated_rds = "${meta.library_id}_processed_annotated.rds"
@@ -190,7 +192,7 @@ workflow annotate_celltypes {
       .mix(classify_singler.out)
 
     // create cellassign input channel: [meta, processed sce, cellassign reference file]
-      cellassign_input_ch = celltype_input_ch
+    cellassign_input_ch = celltype_input_ch
       // add in cellassign reference
       .map{it.toList() + [file(it[0].cellassign_reference_file ?: empty_file)]}
       // skip if no cellassign reference file or reference name is not defined
@@ -234,7 +236,10 @@ workflow annotate_celltypes {
 
 
     // incorporate annotations into SCE object
-    add_celltypes_to_sce(assignment_input_ch.add_celltypes)
+    add_celltypes_to_sce(
+      assignment_input_ch.add_celltypes,
+      file(params.celltype_ref_metadata) // file with CellAssign reference organs
+    )
 
     // mix in libraries without new celltypes
     // result is [meta, proccessed rds]