From 4cb77a4b441394cba0ed1c22d38125f60ab73e53 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 22 Oct 2024 15:29:48 +0200
Subject: [PATCH] Add arguments for filtering methods in benchmark workflow
 (#4)

* Add arguments to filtering methods in benchmark WF

* Apply suggestions from code review

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Tidy method argument definitions

* Move checkMethodAllowed Nexflow helper to common

* Move checkMethodAllowed Nexflow helper to common

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 common                                      |  2 +-
 src/workflows/run_benchmark/config.vsh.yaml | 19 ++++++++++++++++---
 src/workflows/run_benchmark/main.nf         | 11 ++++++++++-
 3 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/common b/common
index e64f472b..dabb6cef 160000
--- a/common
+++ b/common
@@ -1 +1 @@
-Subproject commit e64f472b37f1bdbd383640098708ecf5c9f7fd7e
+Subproject commit dabb6cef9a735e27cfc859a7afc9f5d6685f8635
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index 3ed43a1e..51e482ab 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -42,12 +42,24 @@ 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
@@ -55,6 +67,7 @@ resources:
     entrypoint: run_wf
   - type: file
     path: /_viash.yaml
+  - path: /common/nextflow_helpers/helper.nf
 
 dependencies:
   - name: h5ad/extract_uns_metadata
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
index 2eff6d8d..69322a1a 100644
--- a/src/workflows/run_benchmark/main.nf
+++ b/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(
@@ -75,6 +77,7 @@ workflow run_wf {
   /***************************
    * RUN METHODS AND METRICS *
    ***************************/
+
   score_ch = dataset_ch
 
     // run all methods
@@ -88,7 +91,13 @@ 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
       },