add metrics include / exclude argument

Author: rcannood

CHANGELOG.md

@@ -124,7 +124,7 @@
 
 * Disabled parallelization of `metrics/cms` + cms distributions are now kept in the output AnnData object (PR #83).
 
-* Add arguments for including/excluding methods in the benchmarking workflow (PR #100).
+* Add arguments for including/excluding methods and metrics in the benchmarking workflow (PR #100).
 
 
 ## BUG FIXES

src/workflows/run_benchmark/config.vsh.yaml

@@ -58,6 +58,18 @@ argument_groups:
         multiple: true
         description: |
           A list of method ids to exclude. If specified, all methods except the ones listed will be run.
+  - name: Metrics
+    arguments:
+      - name: "--metrics_include"
+        type: string
+        multiple: true
+        description: |
+          A list of metric ids to include. If specified, only these metrics will be run.
+      - name: "--metrics_exclude"
+        type: string
+        multiple: true
+        description: |
+          A list of metric ids to exclude. If specified, all metrics except the ones listed will be run.
 
 resources:
   - type: nextflow_script

src/workflows/run_benchmark/main.nf

@@ -135,9 +135,15 @@ workflow run_wf {
 
       // run only control methods & filter by method_ids
       filter: { id, state, comp ->
-        def id_filter = !state.method_ids || state.method_ids.contains(comp.config.name)
+        def method_check = checkItemAllowed(
+          comp.config.name,
+          state.methods_include,
+          state.methods_exclude,
+          "methods_include",
+          "methods_exclude"
+        )
         def method_filter = comp.config.info.type == "control_method"
-        id_filter && method_filter
+        method_check && method_filter
       },
 
       // define a new 'id' by appending the method name to the dataset id
@@ -168,6 +174,18 @@ workflow run_wf {
       id: { id, state, comp ->
         id + "." + comp.config.name
       },
+      filter: { id, state, comp ->
+        // filter by metric_ids
+        def metric_check = checkItemAllowed(
+          comp.config.name,
+          state.metrics_include,
+          state.metrics_exclude,
+          "metrics_include",
+          "metrics_exclude"
+        )
+        // filter by method_id
+        metric_check
+      },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
         input_unintegrated: "input_unintegrated",