restructuring viash configs

scripts/run_grn_evaluation.sh

@@ -13,7 +13,7 @@ grn_models_folder="${resources_dir}/grn_models"
 subsample=-2
 max_workers=10
 layer=scgen_pearson
-metric_ids="[regression_1, regression_2]"
+metric_ids="[regression_1]"
 
 param_file="./params/${RUN_ID}.yaml"
 
@@ -67,19 +67,14 @@ append_entry_control() {
     causal: ${2}
     corr_method: ${3}
     prediction: ${resources_dir}/grn_models/collectri.csv
+    cell_type_specific:  ${4}
+    metacell:  ${5}
+    impute: ${6}
 HERE
-  if [ -n "$4" ]; then
-    echo "    cell_type_specific: ${4}" >> $param_file
-  fi
-  if [ -n "$5" ]; then
-    echo "    metacell: ${5}" >> $param_file
-  fi
-  if [ -n "$6" ]; then
-    echo "    impute: ${6}" >> $param_file
-  fi
+
 }
 
-# #Loop through grn_names and layers
+#Loop through grn_names and layers
 # for grn_name in "${grn_names[@]}"; do
 #   append_entry "$grn_name" 
 # done
@@ -88,12 +83,12 @@ HERE
 # append_entry_control "negative_control" "False" ""
 # append_entry_control "positive_control" "False" ""
 # append_entry_control "baseline_pearson" "False" "pearson"
-# append_entry_control "baseline_dotproduct" "False" "dotproduct"
+append_entry_control "baseline_dotproduct" "False" "dotproduct" "false" "false" "false"
 # append_entry_control "baseline_pearson_causal" "True" "pearson" 
-append_entry_control "baseline_dotproduct_causal" "True" "dotproduct" 
+append_entry_control "baseline_dotproduct_causal" "True" "dotproduct" "false" "false" "false"
 # append_entry_control "baseline_dotproduct_causal_cell_type" "True" "dotproduct" "true"
 # append_entry_control "baseline_dotproduct_causal_metacell" "True" "dotproduct" "false" "true"
-append_entry_control "baseline_dotproduct_causal_impute" "True" "dotproduct" "false" "false" "true"
+# append_entry_control "baseline_dotproduct_causal_impute" "True" "dotproduct" "false" "false" "true"
 # append_entry_control "baseline_corr_causal_spearman" "True" "spearman"
 
 

src/api/comp_method.yaml

@@ -10,37 +10,38 @@ functionality:
   arguments:
     - name: --multiomics_rna
       __merge__: file_multiomics_rna_h5ad.yaml
-      required: false
+      required: true
       direction: input
-      default: resources/grn-benchmark/multiomics_rna.h5ad
-    - name: --multiomics_atac
-      __merge__: file_multiomics_atac_h5ad.yaml
-      required: false
-      direction: input
-      must_exist: false
-      default: resources/grn-benchmark/multiomics_atac.h5ad
+      example: resources_test/grn-benchmark/multiomics_rna.h5ad
     - name: --prediction
       __merge__: file_prediction.yaml
-      required: false
+      required: true
       direction: output
-      example: output/prediction.csv
-      default: output/prediction.csv
-    - name: --temp_dir
-      type: string
+      example: resources_test/grn_models/collectri.csv
+    - name: --tf_all
+      type: file
+      required: true
       direction: input
-      default: output/temdir
+      example: resources_test/prior/tf_all.csv
+    - name: --max_n_links
+      type: integer
+      default: 50000
     - name: --num_workers
       type: integer
       direction: input
       default: 4
-    - name: --tf_all
-      type: file
-      example: resources/prior/tf_all.csv
-      default: resources/prior/tf_all.csv
-      required: false
-    - name: --max_n_links
+    - name: --temp_dir
+      type: string
+      direction: input
+      default: output/temdir
+    - name: --seed
       type: integer
-      default: 50000
+      direction: input
+      default: 32
+
+
+
+
 
   test_resources:
     - type: python_script

src/api/comp_method_mo.yaml

@@ -0,0 +1,17 @@
+__merge__: comp_method.yaml
+
+functionality:
+  info:
+    type: methods
+    type_info:
+      label: Method
+      summary: A GRN inference method for multiomics grn
+      description: |
+        A method for inferring GRN from atac and rna data.
+  arguments:
+      - name: --multiomics_atac
+        __merge__: file_multiomics_atac_h5ad.yaml
+        required: true
+        direction: input
+        must_exist: false
+        example: resources_test/grn-benchmark/multiomics_atac.h5ad

src/api/comp_method_r.yaml

@@ -1,5 +1,5 @@
 functionality:
-  namespace: "methods_r"
+  namespace: "methods"
   info:
     type: methods_r
     type_info:

src/api/comp_metric.yaml

@@ -12,17 +12,19 @@ functionality:
       __merge__: file_perturbation_h5ad.yaml
       required: false
       direction: input
-      default: resources/grn-benchmark/perturbation_data.h5ad
     - name: --prediction
       __merge__: file_prediction.yaml
       required: true
       direction: input
-
     - name: --score
       __merge__: file_score.yaml
       required: false
       direction: output
-      default: output/score.h5ad
+    - name: --tf_all
+      type: file
+      direction: input
+      required: true
+      example: resources_test/prior/tf_all.csv
     - name: --reg_type
       type: string
       direction: input
@@ -43,11 +45,6 @@ functionality:
       direction: input 
       required: false
       example: collectri
-    - name: --tf_all
-      type: file
-      direction: input
-      example: resources_test/prior/tf_all.csv
-      default: resources/prior/tf_all.csv
     - name: --apply_tf
       type: boolean 
       required: false
@@ -57,6 +54,11 @@ functionality:
       required: false
       default: true
       description: clips the r2 scores for each gene to make them within [0, 1]
+    - name: --layer
+      type: string
+      direction: input
+      required: false
+      default: scgen_pearson
 
 
 

src/control_methods/baseline_corr/config.vsh.yaml

@@ -1,24 +1,17 @@
-__merge__: ../../api/comp_control_method.yaml
+__merge__: ../../api/comp_method.yaml
 
 functionality:
   name: baseline_corr
+  namespace: control_methods
   info:
     label: baseline_corr
-    summary: "Baseline based on Pearson corr"
+    summary: "Baseline based on correlation"
   arguments:
 
     - name: --causal
       type: boolean 
       direction: input
       default: false
-    - name: --seed
-      type: integer
-      direction: input
-    - name: --multiomics_rna
-      type: file
-      required: true
-      direction: input
-      example: resources_test/grn-benchmark/multiomics_rna.h5ad
     - name: --corr_method
       type: string
       required: false
@@ -50,7 +43,8 @@ platforms:
     image: ghcr.io/openproblems-bio/base_python:1.0.4
     setup:
       - type: python
-        packages: [ magic-impute ]
+        # packages: [ magic-impute ]
+        packages: [  ]
   - type: native
   - type: nextflow
     directives:

src/control_methods/baseline_corr/script.py

@@ -47,7 +47,7 @@ def create_corr_net(X: np.ndarray, groups: np.ndarray, method="pearson"):
     return grn
 print('Read data')
 multiomics_rna = ad.read_h5ad(par["multiomics_rna"])
-# multiomics_rna = multiomics_rna[:,:2000] #TODO: togo
+multiomics_rna = multiomics_rna[:,:2000] #TODO: togo
 
 if par['metacell']:
     print('metacell')

src/control_methods/negative_control/config.vsh.yaml

@@ -1,6 +1,7 @@
-__merge__: ../../api/comp_control_method.yaml
+__merge__: ../../api/comp_method.yaml
 functionality:
   name: negative_control
+  namespace: control_methods
   info:
     label: Negative control
     summary: Source-target links based on random assignment
@@ -9,9 +10,9 @@ functionality:
   arguments:
     - name: --perturbation_data
       type: file
-      required: false
+      required: true
       direction: input
-      default: resources/grn-benchmark/perturbation_data.h5ad
+      example: resources_test/grn-benchmark/perturbation_data.h5ad
 
   resources:
     - type: python_script

src/control_methods/positive_control/config.vsh.yaml

@@ -1,6 +1,7 @@
-__merge__: ../../api/comp_control_method.yaml
+__merge__: ../../api/comp_method.yaml
 functionality:
   name: positive_control
+  namespace: control_methods
   info:
     label: Positive control
     summary: Source-target links based on perturbation data
@@ -9,9 +10,9 @@ functionality:
   arguments:
     - name: --perturbation_data
       type: file
-      required: false
+      required: true
       direction: input
-      default: resources/grn-benchmark/perturbation_data.h5ad
+      example: resources_test/grn-benchmark/perturbation_data.h5ad
 
   resources:
     - type: python_script

src/methods/multi_omics/celloracle/config.vsh.yaml → src/methods/multi_omics/celloracle/config.novsh.yaml

@@ -1,4 +1,4 @@
-__merge__: ../../../api/comp_method.yaml
+__merge__: ../../../api/comp_method_mo.yaml
 
 functionality:
   name: celloracle