Merge pull request #18 from openproblems-bio/fixes

Fixes to wf
openproblems-bio · Feb 6, 2025 · 3ff38ca · 3ff38ca
2 parents 8428344 + 7564f51
commit 3ff38ca
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Showing 3 changed files with 9 additions and 37 deletions.
diff --git a/_viash.yaml b/_viash.yaml
@@ -107,4 +107,4 @@ repositories:
   - name: openproblems
     type: github
     repo: openproblems-bio/openproblems
-    tag: build/main
+    tag: build/main
diff --git a/src/workflows/run_grn_evaluation/config.vsh.yaml b/src/workflows/run_grn_evaluation/config.vsh.yaml
@@ -111,16 +111,14 @@ resources:
   - type: nextflow_script
     path: main.nf
     entrypoint: run_wf
-  - type: file
-    path: /_viash.yaml
 
 
 dependencies:
   - name: metrics/regression_2 
   - name: metrics/regression_1
   - name: metrics/ws_distance
-
-
+  - name: utils/extract_uns_metadata
+    repository: openproblems
 
 runners:
   - type: executable

diff --git a/src/workflows/run_grn_evaluation/main.nf b/src/workflows/run_grn_evaluation/main.nf
@@ -22,41 +22,25 @@ workflow run_wf {
   /***************************
    * RUN METRICS *
    ***************************/
-  score_ch = input_ch
+  output_ch = input_ch
     | map{ id, state ->
         [id, state + ["_meta": [join_id: id]]]
       }
 
-    // | positive_control.run(
-    //   runIf: { id, state ->
-    //     state.method_id == 'positive_control'
-    //   },
-    //   fromState: [
-    //     perturbation_data: "perturbation_data",
-    //     multiomics_rna: "multiomics_rna",
-    //     layer: "layer",
-    //     tf_all: "tf_all"
-    //   ],
-    //   toState: {id, output, state ->
-    //     state + [
-    //       prediction: output.prediction
-    //     ]
-    //   }
-    // )
-
     // run all metrics
     | runEach(
       components: metrics,
       filter: { id, state, comp ->
-        !state.metric_ids || state.metric_ids.contains(comp.config.functionality.name)
+        !state.metric_ids || state.metric_ids.contains(comp.config.name)
       },
       id: { id, state, comp ->
-        id + "." + comp.config.functionality.name
+        id + "." + comp.config.name
       },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
         evaluation_data: "evaluation_data",
         prediction: "prediction",
+        ws_distance_background: "ws_distance_background",
         subsample: "subsample",
         reg_type: "reg_type",
         method_id: "method_id",
@@ -69,16 +53,14 @@ workflow run_wf {
       // use 'toState' to publish that component's outputs to the overall state
       toState: { id, output, state, comp ->
         state + [
-          metric_id: comp.config.functionality.name,
+          metric_id: comp.config.name,
           metric_output: output.score
         ]
       }
     )
 
-  output_ch = score_ch
-
     // extract the scores
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_scores",
       fromState: [input: "metric_output"],
       toState: { id, output, state ->
@@ -96,8 +78,6 @@ workflow run_wf {
       def metric_configs_file = tempFile("metric_configs.yaml")
       metric_configs_file.write(metric_configs_yaml_blob)
 
-      // def task_info_file = meta.resources_dir.resolve("task_info.yaml")
-
       // store the scores in a file
       def score_uns = states.collect{it.score_uns}
       def score_uns_yaml_blob = toYamlBlob(score_uns)
@@ -113,12 +93,6 @@ workflow run_wf {
       ["output", new_state]
     }
 
-    // merge all of the output data 
-    | joinStates{ ids, states ->
-      def mergedStates = states.inject([:]) { acc, m -> acc + m }
-      [ids[0], mergedStates]
-    }
-
   emit:
   output_ch
 }