Adding to API file for exp correction and fixing comments

Author: Habib Rehman

src/api/comp_method_expression_correction.yaml

@@ -15,6 +15,10 @@ arguments:
     required: false
     direction: input
     __merge__: /src/api/file_scrnaseq_reference.yaml
+  - name: --input_ist
+    direction: input
+    required: false
+    __merge__: /src/api/file_transcript_assignments.yaml
   - name: --output
     required: true
     direction: output

src/methods_expression_correction/denoist_correction/config.vsh.yaml

@@ -12,11 +12,6 @@ references:
   doi: "10.1101/2025.11.13.688387"
 
 arguments:
-  - name: --input_ist
-    direction: input
-    required: true
-    type: file
-
   - name: --celltype_key
     required: false
     direction: input

src/methods_expression_correction/denoist_correction/script.R

@@ -11,7 +11,7 @@ par <- list(
   "input_spatial_with_cell_types" = "task_ist_preprocessing/resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_aggregated_counts.h5ad",
   "input_ist" = "task_ist_preprocessing/resources_test/task_ist_preprocessing/mouse_brain_combined/raw_ist.zarr",
   "output" = "task_ist_preprocessing/tmp/denoist_corrected.h5ad",
-#   "keep_all_cells" = FALSE,
+  "keep_all_cells" = FALSE,
   "distance" = 50,
   "nbins" = 200,
 )
@@ -22,7 +22,7 @@ meta <- list(
 
 ## VIASH END
 
-# Read the input h5ad file and convert to SingleCellExperiment and Seurat
+# Read the input h5ad file and convert to SingleCellExperiment -> SpatialExperiment
 cat("Reading input files\n")
 sce <- read_h5ad(par$input_spatial_with_cell_types, as = "SingleCellExperiment")
 
@@ -58,7 +58,7 @@ res <- denoist(mat = spe,
               tx = tx,
               feature_label = "feature_name",
               coords = NULL,
-              distance = par$distance, nbins = par$nbins, cl = cores) #TODO add in params
+              distance = par$distance, nbins = par$nbins, cl = cores)
 
 # format name
 corrected_counts <- res$adjusted_counts