viash file of tf binidng fixed

Author: janursa

src/api/comp_control_method.yaml

@@ -46,7 +46,7 @@ arguments:
   - name: --layer
     type: string
     direction: input
-    default: X_norm
+    default: lognorm
   - name: --seed
     type: integer
     direction: input

src/api/comp_method.yaml

@@ -39,7 +39,7 @@ arguments:
   - name: --layer
     type: string
     direction: input
-    default: X_norm
+    default: lognorm
   - name: --seed
     type: integer
     direction: input

src/api/comp_metric.yaml

@@ -23,7 +23,7 @@ arguments:
     type: string
     direction: input
     required: false
-    default: X_norm
+    default: lognorm
   - name: --max_n_links
     type: integer
     default: 50000

src/metrics/tf_binding/run_local.sh

@@ -39,11 +39,11 @@ for dataset in "${datasets[@]}"; do
         fi
 
         echo -e "\nProcessing method: $method\n"
-        # python src/metrics/tf_binding/script.py \
-        #     --prediction "$prediction" \
-        #     --evaluation_data "$evaluation_data" \
-        #     --ground_truth "resources/grn_benchmark/ground_truth/K562.csv" \
-        #     --score "$score"
+        python src/metrics/tf_binding/script.py \
+            --prediction "$prediction" \
+            --evaluation_data "$evaluation_data" \
+            --ground_truth "resources/grn_benchmark/ground_truth/K562.csv" \
+            --score "$score"
 
         # Extract metrics from the .h5ad and append to CSV
         python -u - <<EOF

src/metrics/tf_recovery/config.vsh.yaml

@@ -12,7 +12,7 @@ arguments:
     direction: input
     must_exist: false
     required: false
-    example: resources_test/grn_benchmark/evaluation_data/replogle_de.csv 
+    example: resources_test/grn_benchmark/evaluation_data/replogle_de.h5ad 
 
 
 resources:
@@ -28,7 +28,7 @@ engines:
     __merge__: /src/api/base_requirements.yaml
     setup:
       - type: python
-        packages: [ decoupler]
+        packages: [ decoupler==1.7.0]
 runners:
   - type: executable
   - type: nextflow