add metrics_include/exclude args

Author: rcannood

CHANGELOG.md

@@ -4,7 +4,7 @@
 
 <!-- * Restructured `src` directory (PR #3). -->
 
-* `run_benchmark`: replaced the `--method_ids` argument with `--methods_include` and `--methods_exclude`, filtered via `checkItemAllowed()` from the common nextflow helpers (PR #20).
+* `run_benchmark`: replaced `--method_ids` with `--methods_include`/`--methods_exclude` and added `--metrics_include`/`--metrics_exclude` (PR #20).
 
 ## NEW FUNCTIONALITY
 

src/workflows/run_benchmark/config.vsh.yaml

@@ -65,6 +65,24 @@ argument_groups:
         multiple: true
         description: |
           A list of method ids to exclude. If specified, all methods except the ones listed will be run.
+  - name: Metric filtering
+    description: |
+      Use these arguments to filter metrics by name. By default, all metrics are
+      run. If `--metrics_include` is defined, only those metrics are run. If
+      `--metrics_exclude` is defined, all metrics except those specified are run.
+      These arguments are mutually exclusive, so only `--metrics_include` OR
+      `--metrics_exclude` can set but not both.
+    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

@@ -99,6 +99,18 @@ workflow run_wf {
     // run all metrics
     | runEach(
       components: metrics,
+
+      // use the 'filter' argument to only run the metrics the user asked for
+      filter: { id, state, comp ->
+        checkItemAllowed(
+          comp.config.name,
+          state.metrics_include,
+          state.metrics_exclude,
+          "metrics_include",
+          "metrics_exclude"
+        )
+      },
+
       id: { id, state, comp ->
         id + "." + comp.config.name
       },