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AzureInfrastructure.md

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Azure infrastructure

Key Vault

With the following secrets created:

  • azure-registry-server
  • azure-registry-username
  • azure-registry-password
  • azure-batch-location
  • azure-batch-accountName
  • azure-batch-accountKey
  • azure-storage-accountName
  • azure_storage_accountName
  • azure-storage-accountKey
  • azure_storage_accountKey

Container Registry

  • Nextflow image built and pushed to registry.
  • Ubuntu image built and pushed to registry.
  • Admin user enabled and keys stored in Key Vault.

Storage Account

  • Storage blob with 'batch' container created.
  • Storage files with 'batchsmb' share created.
  • Keys enabled and stored in Key Vault.

Managed Identities

  • Create a Managed Identity for Batch Account 'batchmid'.
  • Create a Managed Identity for nextflow Container Instance(s) 'nextflowmid'

Batch Account

  • Pool allocation mode set to "Batch service".
  • Connected to above Storage Account using User Assigned Managed Identity.
  • Keys enabled and stored in Key Vault.

Container Instance

  • Configured using the nextflow image.
  • Read access granted in Key Vault using User Assigned Managed Identity.
  • Override the "AZ_KEY_VAULT_NAME" environment variable with the name of the Key Vault resource.
  • Override the "AZURE_CLIENT_ID" environment variable with the client id of the nextflowmid Managed Identity resource.
  • (optional) Override the CMD with one similar to that below to execute a different Nextflow pipeline. 
    cd /.nextflow && \
./nxfutil -c "https://<...>/nextflow.config" \
    -p "https://<...>/pipeline.nf" \
    -a "https://<...>/parameters.json"