fix wf

Author: rcannood

src/api/comp_data_preprocessor.yaml

@@ -16,11 +16,11 @@ arguments:
     __merge__: file_common_scrnaseq.yaml
     direction: input
     required: true
-  - name: "--output_ist"
+  - name: "--output_sp"
     __merge__: file_raw_ist.yaml
     direction: output
     required: true
-  - name: "--output_scrnaseq"
+  - name: "--output_sc"
     __merge__: file_scrnaseq_reference.yaml
     direction: output
     required: true

src/workflows/process_datasets/main.nf

@@ -14,31 +14,19 @@ workflow run_wf {
   main:
   output_ch = input_ch
 
-    // example of channel event: 
-    //   ["mouse_brain_combined", [
-    //      "input_sc": file("resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad"),
-    //      "input_sp": file("resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr")]]
-
     | process_dataset_comp.run(
       fromState: [
-        input_ist: "input_sp",
-        input_scrnaseq: "input_sc"
+        input_sp: "input_sp",
+        input_sc: "input_sc"
       ],
       toState: [
-        output_sc: "output_scrnaseq",
-        output_sp: "output_ist"
+        output_sc: "output_sc",
+        output_sp: "output_sp"
       ]
     )
 
-    // example of channel event at this point:
-    //   ["my_id", ["input_sc": ..., "input_sp": ..., 
-    //              "output_sc": file("..."), "output_sp": file("...")]]
-
     | setState(["output_sp", "output_sc"])
 
-    // example of channel event at this point:
-    //   ["my_id", ["output_sc": file("..."), "output_sp": file("...")]]
-
   emit:
   output_ch
 }