fix components

Author: rcannood

scripts/create_resources/process_datasets.sh

@@ -20,8 +20,8 @@ param_list:
   - id: "mouse_brain_combined/rep2"
     input_sp: "$input_dir/10x_xenium/2023_10x_mouse_brain_xenium/rep2/dataset.zarr"
     input_sc: "$input_dir/allen_brain_cell_atlas/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad"
-  - id: "mouse_brain_combined/rep2"
-    input_sp: "$input_dir/10x_xenium/2023_10x_mouse_brain_xenium/rep2/dataset.zarr"
+  - id: "mouse_brain_combined/rep3"
+    input_sp: "$input_dir/10x_xenium/2023_10x_mouse_brain_xenium/rep3/dataset.zarr"
     input_sc: "$input_dir/allen_brain_cell_atlas/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad"
 
 output_sc: "\$id/output_sc.h5ad"

src/api/comp_data_preprocessor.yaml

@@ -8,11 +8,11 @@ info:
       This component processes a common single-cell and a common spatial transcriptomics
       dataset for the benchmark.
 arguments:
-  - name: "--input_ist"
+  - name: "--input_sp"
     __merge__: file_common_ist.yaml
     direction: input
     required: true
-  - name: "--input_scrnaseq"
+  - name: "--input_sc"
     __merge__: file_common_scrnaseq.yaml
     direction: input
     required: true

src/data_processors/process_dataset/script.py

@@ -6,18 +6,18 @@
 
 ### VIASH START
 par = {
-  "input_scrnaseq": "resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad",
-  "input_ist": "resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr",
+  "input_sc": "resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad",
+  "input_sp": "resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr",
   "output_scrnaseq": "resources_test/task_ist_preprocessing/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad",
   "output_ist": "resources_test/task_ist_preprocessing/2023_10x_mouse_brain_xenium_rep1/dataset.zarr"
 }
 ### VIASH END
 
 # Load the single-cell data
-adata = ad.read_h5ad(par["input_scrnaseq"])
+adata = ad.read_h5ad(par["input_sc"])
 
 # Load the spatial data
-sdata = sd.read_zarr(par["input_ist"])
+sdata = sd.read_zarr(par["input_sp"])
 
 # Subset the single-cell data to spatial genes
 genes_sp = []

src/datasets/loaders/allen_brain_cell_atlas/script.py

@@ -161,4 +161,4 @@
 print(f"Output: {adata}")
 
 # Write data
-adata.write_h5ad(par["output"])
+adata.write_h5ad(par["output"], compression="gzip")