failed so methods updated

scripts/run_benchmark_single_omics.sh

@@ -1,23 +1,27 @@
 #!/bin/bash
 
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-RUN_ID="single_omics_scgpt"
-# resources_dir="./resources_test/"
-resources_dir="s3://openproblems-data/resources_test/grn"
+RUN_ID="single_omics_test"
+resources_dir="./resources_test/"
+# resources_dir="s3://openproblems-data/resources_test/grn"
 publish_dir="${resources_dir}/results/${RUN_ID}"
 
 
 reg_type=ridge
 subsample=-2
 max_workers=10
 layer='pearson'
+metric_ids="[regression_1, regression_2]"
+method_ids="[tigress, ennet, scsgl]"
 
 param_file="./params/${RUN_ID}.yaml"
 
 # Start writing to the YAML file
 cat > $param_file << HERE
 param_list:
   - id: ${reg_type}
+    metric_ids: $metric_ids
+    method_ids: $method_ids
     perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad
     multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
     reg_type: $reg_type
@@ -34,12 +38,12 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-# nextflow run . \
-#   -main-script  target/nextflow/workflows/run_benchmark_single_omics/main.nf \
-#   -profile docker \
-#   -with-trace \
-#   -c src/common/nextflow_helpers/labels_ci.config \
-#   -params-file ${param_file}
+nextflow run . \
+  -main-script  target/nextflow/workflows/run_benchmark_single_omics/main.nf \
+  -profile docker \
+  -with-trace \
+  -c src/common/nextflow_helpers/labels_ci.config \
+  -params-file ${param_file}
 
 # ./tw-windows-x86_64.exe launch `
 #     https://github.com/openproblems-bio/task_grn_inference.git `

src/api/comp_control_method.yaml

@@ -9,16 +9,6 @@ functionality:
       description: |
         A control method to serve as a quality control for the GRN inference benchmark.
   arguments:
-    - name: --perturbation_data
-      __merge__: file_perturbation_h5ad.yaml
-      required: false
-      direction: input
-      default: resources/grn-benchmark/perturbation_data.h5ad
-    - name: --multiomics_rna
-      __merge__: file_multiomics_rna_h5ad.yaml
-      required: false
-      direction: input
-      example: resources_test/grn-benchmark/multiomics_rna.h5ad
     - name: --layer
       type: string
       direction: input

src/control_methods/baseline_corr/config.vsh.yaml

@@ -14,7 +14,11 @@ functionality:
     - name: --seed
       type: integer
       direction: input
-
+    - name: --multiomics_rna
+      type: file
+      required: false
+      direction: input
+      example: resources_test/grn-benchmark/multiomics_rna.h5ad
   resources:
     - type: python_script
       path: script.py

src/control_methods/negative_control/config.vsh.yaml

@@ -6,6 +6,13 @@ functionality:
     summary: Source-target links based on random assignment
     description: |
       Randomly assigns regulatory links to tf-target links with a given tf and target list. This is to perform near random.
+  arguments:
+    - name: --perturbation_data
+      type: file
+      required: false
+      direction: input
+      default: resources/grn-benchmark/perturbation_data.h5ad
+
   resources:
     - type: python_script
       path: script.py

src/control_methods/positive_control/config.vsh.yaml

@@ -6,6 +6,12 @@ functionality:
     summary: Source-target links based on perturbation data
     description: |
       By directly training on perturbation data, positive control is expected to learn more accurate tf-gene connections.
+  arguments:
+    - name: --perturbation_data
+      type: file
+      required: false
+      direction: input
+      default: resources/grn-benchmark/perturbation_data.h5ad
 
   resources:
     - type: python_script

src/workflows/run_benchmark_single_omics/main.nf

@@ -13,22 +13,22 @@ workflow run_wf {
 
   // construct list of methods
   methods = [
-    portia
-    ennet
-    genie3
-    grnboost2
-    pidc
-    ppcor
-    scsgl
-    tigress
+    portia,
+    ennet,
+    genie3,
+    grnboost2,
+    pidc,
+    ppcor,
+    scsgl,
+    tigress,
     scgpt
   ]
 
 
   // construct list of metrics
   metrics = [
     regression_1,
-    regression_2,
+    regression_2
   ]
 
   /****************************