From 2077bdaf9ff05f7c9400f333d8759273a6f2e455 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 2 Sep 2024 10:25:42 +0200
Subject: [PATCH] disable invalid __merge__ statements

---
 .../process_dataset/config.vsh.yaml           |   2 +-
 .../process_datasets/config.vsh.yaml          |  40 +++----
 src/workflows/run_benchmark/config.vsh.yaml   | 102 +++++++++---------
 3 files changed, 72 insertions(+), 72 deletions(-)

diff --git a/src/data_processors/process_dataset/config.vsh.yaml b/src/data_processors/process_dataset/config.vsh.yaml
index 7155c60..09b8b71 100644
--- a/src/data_processors/process_dataset/config.vsh.yaml
+++ b/src/data_processors/process_dataset/config.vsh.yaml
@@ -1,4 +1,4 @@
-__merge__: ../../api/comp_data_processor.yaml
+__merge__: /src/api/comp_process_dataset.yaml
 name: process_dataset
 status: disabled
 arguments:
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 2c4e9f7..7000eb8 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -4,26 +4,26 @@ namespace: workflows
 status: disabled
 
 argument_groups:
-  - name: Inputs
-    arguments:
-      - name: "--input"
-        __merge__: /src/api/file_common_dataset.yaml
-        required: true
-        direction: input
-  - name: Outputs
-    arguments:
-      - name: "--output_train"
-        __merge__: /src/api/file_train_h5ad.yaml
-        required: true
-        direction: output
-      - name: "--output_test"
-        __merge__: /src/api/file_test_h5ad.yaml
-        required: true
-        direction: output
-      - name: "--output_solution"
-        __merge__: /src/api/file_solution.yaml
-        required: true
-        direction: output
+  # - name: Inputs
+  #   arguments:
+  #     - name: "--input"
+  #       __merge__: /src/api/file_common_dataset.yaml
+  #       required: true
+  #       direction: input
+  # - name: Outputs
+  #   arguments:
+  #     - name: "--output_train"
+  #       __merge__: /src/api/file_train_h5ad.yaml
+  #       required: true
+  #       direction: output
+  #     - name: "--output_test"
+  #       __merge__: /src/api/file_test_h5ad.yaml
+  #       required: true
+  #       direction: output
+  #     - name: "--output_solution"
+  #       __merge__: /src/api/file_solution.yaml
+  #       required: true
+  #       direction: output
 
 resources:
   - type: nextflow_script
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index e28f628..1976ed4 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -4,57 +4,57 @@ namespace: workflows
 status: disabled
 
 argument_groups:
-  - name: Inputs
-    arguments:
-      - name: "--input_train"
-        __merge__: /src/api/file_train_h5ad.yaml
-        type: file
-        direction: input
-        required: true
-      - name: "--input_test"
-        __merge__: /src/api/file_test_h5ad.yaml
-        type: file
-        direction: input
-        required: true
-      - name: "--input_solution"
-        __merge__: /src/api/file_solution.yaml
-        type: file
-        direction: input
-        required: true
-  - name: Outputs
-    arguments:
-      - name: "--output_scores"
-        type: file
-        required: true
-        direction: output
-        description: A yaml file containing the scores of each of the methods
-        default: score_uns.yaml
-      - name: "--output_method_configs"
-        type: file
-        required: true
-        direction: output
-        default: method_configs.yaml
-      - name: "--output_metric_configs"
-        type: file
-        required: true
-        direction: output
-        default: metric_configs.yaml
-      - name: "--output_dataset_info"
-        type: file
-        required: true
-        direction: output
-        default: dataset_uns.yaml
-      - name: "--output_task_info"
-        type: file
-        required: true
-        direction: output
-        default: task_info.yaml
-  - name: Methods
-    arguments:
-      - name: "--method_ids"
-        type: string
-        multiple: true
-        description: A list of method ids to run. If not specified, all methods will be run.
+  # - name: Inputs
+  #   arguments:
+  #     - name: "--input_train"
+  #       __merge__: /src/api/file_train_h5ad.yaml
+  #       type: file
+  #       direction: input
+  #       required: true
+  #     - name: "--input_test"
+  #       __merge__: /src/api/file_test_h5ad.yaml
+  #       type: file
+  #       direction: input
+  #       required: true
+  #     - name: "--input_solution"
+  #       __merge__: /src/api/file_solution.yaml
+  #       type: file
+  #       direction: input
+  #       required: true
+  # - name: Outputs
+  #   arguments:
+  #     - name: "--output_scores"
+  #       type: file
+  #       required: true
+  #       direction: output
+  #       description: A yaml file containing the scores of each of the methods
+  #       default: score_uns.yaml
+  #     - name: "--output_method_configs"
+  #       type: file
+  #       required: true
+  #       direction: output
+  #       default: method_configs.yaml
+  #     - name: "--output_metric_configs"
+  #       type: file
+  #       required: true
+  #       direction: output
+  #       default: metric_configs.yaml
+  #     - name: "--output_dataset_info"
+  #       type: file
+  #       required: true
+  #       direction: output
+  #       default: dataset_uns.yaml
+  #     - name: "--output_task_info"
+  #       type: file
+  #       required: true
+  #       direction: output
+  #       default: task_info.yaml
+  # - name: Methods
+  #   arguments:
+  #     - name: "--method_ids"
+  #       type: string
+  #       multiple: true
+  #       description: A list of method ids to run. If not specified, all methods will be run.
 
 resources:
   - type: nextflow_script