use methods_include/exclude args

Author: rcannood

src/workflows/run_benchmark/config.vsh.yaml

@@ -47,19 +47,32 @@ 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: utils/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(
@@ -57,7 +59,13 @@ 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
       },