[GEN-1574] Add merge and decode to staging #161
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rxu17
changed the title
danlu1
requested changes
Oct 31, 2024
thomasyu888
reviewed
Nov 1, 2024
| @@ -13,7 +13,7 @@ jobs: | |||
| runs-on: ubuntu-latest | |||
| strategy: | |||
| matrix: | |||
| module: ["references", "table_updates"] # Define the modules you want to loop through for builds | |||
| module: ["references", "table_updates", "uploads"] # Define the modules you want to loop through for builds | |||
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This is wonderful! Yay for scalable solutions!
thomasyu888
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Nov 1, 2024
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| make_option(c("-a", "--synapse_auth"), type = "character", default = NA, | ||
| help="Path to .synapseConfig file or Synapse PAT (default: normal synapse login behavior)"), |
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Nit: don't need to do this now, but in the future if you see these, it can all be removed since we added support SYNAPSE_AUTH_TOKEN style login to the synapse client.
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Purpose: We currently don't have a way to safely test and upload results to non-production environment for
merge_and_decodestep in genie bpc pipeline. This is to add that.Changes:
Aside from the nextflow workflow changes, here are the relevant changes in the
merge_and_uncode_rca_uploads.Rscript:productionflag and logic surrounding it to retrieve the correct entities for staging vs productionTesting:
get_output_folder_iddevelopbranch docker (except changed the synapse id of the output to staging) and compared it to results on the feature branch docker and no differences found!