workflow updated: single grn benchmark

scripts/run_grn_evaluation.sh

@@ -39,6 +39,7 @@ append_entry() {
   - id: ${reg_type}_${1}
     metric_ids: ${metric_ids}
     perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad
+    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
     reg_type: $reg_type
     method_id: $1
     subsample: $subsample

src/api/comp_control_method.yaml

@@ -14,11 +14,6 @@ functionality:
       required: false
       direction: input
       default: resources/grn-benchmark/perturbation_data.h5ad
-    - name: --multiomics_rna
-      __merge__: file_multiomics_rna_h5ad.yaml
-      required: false
-      direction: input
-      default: resources/grn-benchmark/multiomics_rna.h5ad
     - name: --layer
       type: string
       direction: input

src/control_methods/baseline_corr/config.vsh.yaml

@@ -7,6 +7,9 @@ functionality:
     summary: "Baseline based on Pearson corr"
 
   arguments:
+    - name: --multiomics_rna
+      required: false
+      direction: input
     - name: --causal
       type: boolean 
       direction: input

src/methods/single_omics/ennet/config.vsh.yaml

@@ -34,4 +34,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [threedaystime,midmem,midcpu]
+      label: [onedaytime,midmem,midcpu]

src/methods/single_omics/pidc/config.vsh.yaml

@@ -22,4 +22,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [threedaystime, midmem,midcpu]
+      label: [onedaytime, midmem,midcpu]

src/methods/single_omics/scsgl/config.vsh.yaml

@@ -22,4 +22,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [threedaystime, midmem,midcpu]
+      label: [onedaytime, midmem,midcpu]

src/methods/single_omics/tigress/config.vsh.yaml

@@ -30,4 +30,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [threedaystime, midmem, highcpu]
+      label: [onedaytime, midmem, highcpu]

src/workflows/run_benchmark_single_omics/config.vsh.yaml

@@ -71,6 +71,16 @@ functionality:
         #   required: true
         #   direction: output
         #   default: metric_configs.yaml
+    - name: Arguments
+      arguments: 
+        - name: "--method_ids"
+          type: string
+          multiple: true
+          description: A list of method ids to run. If not specified, all methods will be run.
+        - name: "--metric_ids"
+          type: string
+          multiple: true
+          description: A list of metric ids to run. If not specified, all metric will be run.
 
   resources:
     - type: nextflow_script

src/workflows/run_benchmark_single_omics/main.nf

@@ -13,21 +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_1,
+    regression_2,
   ]
 
   /****************************
@@ -57,6 +58,9 @@ workflow run_wf {
     // run all methods
     | runEach(
       components: methods,
+      filter: { id, state, comp ->
+        !state.method_ids || state.method_ids.contains(comp.config.functionality.name)
+      },
 
       // use the 'filter' argument to only run a defined method or all methods
       // filter: { id, state, comp ->
@@ -91,6 +95,9 @@ workflow run_wf {
     // run all metrics
     | runEach(
       components: metrics,
+      filter: { id, state, comp ->
+        !state.metric_ids || state.metric_ids.contains(comp.config.functionality.name)
+      },
       id: { id, state, comp ->
         id + "." + comp.config.functionality.name
       },

src/workflows/run_grn_evaluation/main.nf

@@ -93,12 +93,12 @@ workflow run_wf {
     // run all metrics
     | runEach(
       components: metrics,
-      id: { id, state, comp ->
-        id + "." + comp.config.functionality.name
-      },
       filter: { id, state, comp ->
         !state.metric_ids || state.metric_ids.contains(comp.config.functionality.name)
       },
+      id: { id, state, comp ->
+        id + "." + comp.config.functionality.name
+      },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
         perturbation_data: "perturbation_data",