change to workflow run benchmark

src/api/comp_metric.yaml

@@ -49,11 +49,7 @@ functionality:
       type: boolean 
       required: false
       default: true
-    - name: --clip_scores
-      type: boolean 
-      required: false
-      default: true
-      description: clips the r2 scores for each gene to make them within [0, 1]
+
     - name: --layer
       type: string
       direction: input

src/api/unit_test.yaml

@@ -2,5 +2,5 @@ functionality:
   test_resources:
     - type: python_script
       path: /src/common/component_tests/run_and_check_output.py
-    - path: /resources_test/grn-benchmark
-      dest: resources_test/grn-benchmark
+    - path: /resources_test/
+      dest: resources_test/

src/metrics/script_all.py

@@ -69,16 +69,16 @@ def define_par(dataset):
 global_models = False
 
 # - run metrics 
-for dataset in ['op']: #'op', 'replogle2', 'nakatake', 'norman', 'adamson'
+for dataset in ['op', 'replogle2', 'nakatake', 'norman', 'adamson']: #'op', 'replogle2', 'nakatake', 'norman', 'adamson'
   print('------ ', dataset, '------')
   par = define_par(dataset)
   os.makedirs(par['scores_dir'], exist_ok=True)
   main_consensus(par)
   for binarize in [True]:
     par['binarize'] = binarize
-    for max_n_links in [50000]:
+    for max_n_links in [10000]:
       par['max_n_links'] = max_n_links
-      for apply_skeleton in [True]:
+      for apply_skeleton in [False]:
         par['apply_skeleton'] = apply_skeleton
         # - determines models to run 
         grn_files_dict = {}

src/workflows/run_benchmark/config.vsh.yaml

@@ -88,9 +88,7 @@ functionality:
     - name: grn_methods/portia
     - name: grn_methods/grnboost2
     - name: grn_methods/scenic
-
     # - name: grn_methods/genie3
-
     - name: grn_methods/ppcor #needs docker image
     - name: grn_methods/scgpt 
 

src/workflows/run_benchmark/main.nf

@@ -19,6 +19,7 @@ workflow run_wf {
     ppcor,
     scenic,
     scglue,
+    scgpt,
 
     pearson_corr,
     negative_control,