Allow setting data managers parameters in genomes.yml

galaxyproject · Feb 2, 2024 · 9ba1626 · 9ba1626
1 parent 413d156
commit 9ba1626
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/src/ephemeris/_config_models.py b/src/ephemeris/_config_models.py
@@ -45,6 +45,7 @@ class RepositoryInstallTargets(BaseModel):
 class DataManager(BaseModel, extra=Extra.forbid):
     tags: List[str]
     tool_id: str
+    parameters: Optional[List[Dict[str, str]]] = None
 
 
 class DataManagers(BaseModel, extra=Extra.forbid):

diff --git a/src/ephemeris/_idc_split_data_manager_genomes.py b/src/ephemeris/_idc_split_data_manager_genomes.py
@@ -222,11 +222,14 @@ def walk_over_incomplete_runs(split_options: SplitOptions):
             log.info(f"Building: {build_id} {indexer}")
 
             tool_id = tool_id_for(indexer, data_managers, split_options.tool_id_mode)
-            params = [
-                {"all_fasta_source": "{{ item.id }}"},
-                {"sequence_name": "{{ item.name }}"},
-                {"sequence_id": "{{ item.id }}"},
-            ]
+            data_manager = data_managers.__root__[indexer]
+            params = data_manager.parameters
+            if params is None:
+                params = [
+                    {"all_fasta_source": "{{ item.id }}"},
+                    {"sequence_name": "{{ item.name }}"},
+                    {"sequence_id": "{{ item.id }}"},
+                ]
             # why is this not pulled from the data managers conf? -nate
             if re.search("bwa", tool_id):
                 params.append({"index_algorithm": "bwtsw"})