Redefine service-provided input paths (#134)

service/src/main/resources/db/changelog.xml

@@ -27,6 +27,7 @@
   <include file="changesets/20240903_rename_workspace_project.yaml" relativeToChangelogFile="true"/>
   <include file="changesets/20240906_add_wdl_version_to_pipeline_run.yaml" relativeToChangelogFile="true"/>
   <include file="changesets/20240911_remove_isSuccess.yaml" relativeToChangelogFile="true"/>
+  <include file="changesets/20240923_update_input_defs_bucket_paths.yaml" relativeToChangelogFile="true"/>
 
   <include file="changesets/20240412-testdata.yaml" relativeToChangelogFile="true"/>
 

service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml

@@ -0,0 +1,30 @@
+# Update input definitions bucket paths for service provided inputs
+databaseChangeLog:
+  - changeSet:
+      id: Update input definitions bucket paths for service provided inputs
+      author: mma
+      changes:
+        # update geneticMapsPath default_value from /plink-genetic-maps/GRCh38_fixed/
+        - update:
+            tableName: pipeline_input_definitions
+            where: name='geneticMapsPath' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/plink-genetic-maps/"
+        # update refDict default_value from /hg38/Homo_sapiens_assembly38.dict
+        - update:
+            tableName: pipeline_input_definitions
+            where: name='refDict' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/ref_dict/Homo_sapiens_assembly38.dict"
+        # update referencePanelPathPrefix default_value from /hg38/1000G_HGDP_no_singletons_ref_panel/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2
+        - update:
+            tableName: pipeline_input_definitions
+            where: name='referencePanelPathPrefix' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/ref_panels/1000G_HGDP_no_singletons/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2"