Add arguments for filtering methods in benchmark workflow

src/workflows/run_benchmark/config.vsh.yaml

@@ -42,19 +42,32 @@ argument_groups:
         required: true
         direction: output
         default: task_info.yaml
-  - name: Methods
+  - name: Method filtering
+    description: |
+      Use these arguments to filter methods by name. By default, all methods are
+      run. If `--methods_include` is defined, only those methods are run. If
+      `--methods_exclude` is defined, all methods except those specified are run.
+      These arguments are mutually exclusive, so only `--methods_include` OR
+      `--methods_exclude` can set but not both.
     arguments:
-      - name: "--method_ids"
+      - name: "--methods_include"
         type: string
         multiple: true
-        description: A list of method ids to run. If not specified, all methods will be run.
+        description: |
+          A list of method ids to include. If specified, only these methods will be run.
+      - name: "--methods_exclude"
+        type: string
+        multiple: true
+        description: |
+          A list of method ids to exclude. If specified, all methods except the ones listed will be run.
 
 resources:
   - type: nextflow_script
     path: main.nf
     entrypoint: run_wf
   - type: file
     path: /_viash.yaml
+  - path: /common/nextflow_helpers/helper.nf
 
 dependencies:
   - name: h5ad/extract_uns_metadata

src/workflows/run_benchmark/main.nf

@@ -1,3 +1,5 @@
+include { checkItemAllowed } from "${meta.resources_dir}/helper.nf"
+
 workflow auto {
   findStates(params, meta.config)
     | meta.workflow.run(
@@ -55,7 +57,7 @@ workflow run_wf {
    ****************************/
   dataset_ch = input_ch
     // store join id
-    | map{ id, state -> 
+    | map{ id, state ->
       [id, state + ["_meta": [join_id: id]]]
     }
 
@@ -72,6 +74,7 @@ workflow run_wf {
   /***************************
    * RUN METHODS AND METRICS *
    ***************************/
+
   score_ch = dataset_ch
 
     // run all methods
@@ -85,7 +88,13 @@ workflow run_wf {
         // if the preferred normalisation is none at all,
         // we can pass whichever dataset we want
         def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref
-        def method_check = !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"
+        )
 
         method_check && norm_check
       },
@@ -153,7 +162,7 @@ workflow run_wf {
       },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
-        input_solution: "input_solution", 
+        input_solution: "input_solution",
         input_integrated: "method_output_cleaned"
       ],
       // use 'toState' to publish that component's outputs to the overall state