cellassign reference file variable name

AlexsLemonade · Oct 3, 2023 · 4ada0c8 · 4ada0c8
1 parent 6ee6043
commit 4ada0c8
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
@@ -60,14 +60,14 @@ process classify_cellassign {
     
     # Convert SCE to AnnData
     sce_to_anndata.R \
-        --input_sce_file ${processed_rds} \
+        --input_sce_file "${processed_rds}" \
         --output_rna_h5 processed.hdf5 
         
     # Run CellAssign
     predict_cellassign.py \
       --input_hdf5_file processed.hdf5 
-      --output_predictions ${cellassign_dir}/cellassign_predictions.tsv \
-      --reference ${cellassign_ref} \
+      --output_predictions "${cellassign_dir}/cellassign_predictions.tsv" \
+      --reference "${cellassign_reference_file} \
       --seed ${params.seed} \
       --threads ${task.cpus}