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MS Genomics

The Microsoft Genomics Service task type allows for MS Genomics workflows to be executed as part of a Loome Integrate job.

Installing the MS Genomics Service

The MS Genomics task type will require the msgen CLI to be installed on the agent’s host.

Installation instructions are available here.

Warning

The datagovernor/agent Docker Image does not currently come bundled with the MS Genomics service and so a custom image must be created to allow for execution in Docker.

Creating a Microsoft Genomics Task

The MS Genomics task type requires 3 connections:

  • The Genomics Connection

    • This is the service connection that is used for submitting the genomics workflow.

  • The Source Blob Connection

    • This is the Azure Blob connection that is used for sourcing data that is used by the MS Genomics processor.

  • The Target Blob Connection

    • This is the Azure Blob connection that is used for saving the output created by the MS Genomics Service.

On top of this, you must provide additional parameters which are used in the MS Genomics workflow.

MS Genomics Screen MS Genomics Screen

Required Parameters

Note

To learn more about the MS Genomics processor parameters, read the Microsoft Python Client documentation.

Param Name Description Example Value
process-args Additional arguments to provide the MS Genomics Workflow. R=hg191m1
input-storage-account-container The name of the container which has your input blobs. inputcontainer
output-storage-account-container The name of the container which will store the output from your msgen execution. outputcontainer
input-blob-name-1 The name of one of the input blobs to pass into msgen. chr21_1.fq.gz
input-blob-name-2 The name of one of the input blobs to pass into msgen. chr21_2.fq.gz