Redefine service-provided input paths

[mmorgantaylor]

Description

Updating the default_value for service-provided input files to match the organization we want. This includes an hg38 prefix for all, plus different intermediate "directory" files in some cases

Changes:

• geneticMapsPath
  • old value: /plink-genetic-maps/GRCh38_fixed/
  • new value: /hg38/plink-genetic-maps/
• refDict
  • old value: /hg38/Homo_sapiens_assembly38.dict
  • new value: /hg38/ref_dict/Homo_sapiens_assembly38.dict
• referencePanelPathPrefix
  • old value: /hg38/1000G_HGDP_no_singletons_ref_panel/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2
  • new value: /hg38/ref_panels/1000G_HGDP_no_singletons/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2

Also performed the copy of these files in the dev bucket:

✗ gcloud storage ls gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/plink-genetic-maps/ | wc -l
      22

✗ gcloud storage ls gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/ref_dict/Homo_sapiens_assembly38.dict
gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/ref_dict/Homo_sapiens_assembly38.dict

✗ gcloud storage ls gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/ref_panels/1000G_HGDP_no_singletons/ | wc -l
      66

✗ gcloud storage ls gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/ref_panels/simulated/500k/ | wc -l
     110

✗ gcloud storage ls gs://fc-secure-10efd4d7-392a-4e9e-89ea-d6629fbb06cc/hg38/ref_panels/simulated/10k/ | wc -l
     110

Will need to delete the old copies once the currently running workflows using the old paths have completed.

Jira Ticket

none

[jsotobroad]

nice changes - one small TOL

[jsotobroad]

a slightly better approach would be to do something like where pipeline_id=3 and probably the best approach would be where pipeline_id = (select id from pipelines where name = "imputation_beagle") or w/e the equivalent for liquidbase is. No need for changes though

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud