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Redefine service-provided input paths #134

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Sep 23, 2024
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1 change: 1 addition & 0 deletions service/src/main/resources/db/changelog.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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"/>

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Original file line number Diff line number Diff line change
@@ -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"
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