fix components

scripts/render_readme.sh

@@ -1,11 +1,5 @@
 #!/bin/bash
 
-set -e
-
-[[ ! -d ../openproblems-v2 ]] && echo "You need to clone the openproblems-v2 repository next to this repository" && exit 1
-
-../openproblems-v2/target/docker/common/create_task_readme/create_task_readme \
-  --task "perturbation_prediction" \
-  --task_dir "src" \
-  --github_url "https://github.com/openproblems-bio/task_perturbation_prediction/tree/main/" \
-  --output "README.md"
+common/create_task_readme/create_task_readme \
+  --task_dir src \
+  --output README.md

src/api/wf_method.yaml

@@ -1,32 +1,31 @@
-functionality:
-  namespace: "methods"
-  info:
-    type: method
-    type_info:
-      label: Method
-      summary: A perturbation prediction method
-      description: |
-        A method for predicting the perturbation response of small molecules on certain cell types.
-  arguments:
-    - name: --de_train_h5ad
-      __merge__: file_de_train.yaml
-      required: false
-      direction: input
-    - name: --id_map
-      __merge__: file_id_map.yaml
-      required: true
-      direction: input
-    - name: --layer
-      type: string
-      direction: input
-      default: clipped_sign_log10_pval
-      description: Which layer to use for prediction.
-    - name: --output
-      __merge__: file_prediction.yaml
-      required: true
-      direction: output
-    - name: "--output_model"
-      __merge__: file_model.yaml
-      direction: output
-      required: false
-      must_exist: false
+namespace: "methods"
+info:
+  type: method
+  type_info:
+    label: Method
+    summary: A perturbation prediction method
+    description: |
+      A method for predicting the perturbation response of small molecules on certain cell types.
+arguments:
+  - name: --de_train_h5ad
+    __merge__: file_de_train.yaml
+    required: false
+    direction: input
+  - name: --id_map
+    __merge__: file_id_map.yaml
+    required: true
+    direction: input
+  - name: --layer
+    type: string
+    direction: input
+    default: clipped_sign_log10_pval
+    description: Which layer to use for prediction.
+  - name: --output
+    __merge__: file_prediction.yaml
+    required: true
+    direction: output
+  - name: "--output_model"
+    __merge__: file_model.yaml
+    direction: output
+    required: false
+    must_exist: false