workflows: Interact with the Microsoft Genomics service in Azure

In colbyford/msgen: R functions for interfacing with the Microsoft Genomics Service in Azure

Description

Submit, list, check the status, and cancel genomics workflows in the Microsoft Genomics service in Azure.

Usage

submit_workflow(subscription_key,
       region,
       description = "Submission from msgen R package.",
       process = "snapgatk",
       reference = "hg19m1",
       input_storage_account_name,
       input_storage_account_key,
       input_container_name,
       blob_name_1,
       blob_name_2 = NULL,
       output_storage_account_name,
       output_storage_account_key,
       output_container_name)
       
list_workflows(subscription_key,
     region)
          
get_workflow_status(subscription_key,
       region,
       workflow_id = NULL)
          
cancel_workflow(subscription_key,
       region,
       workflow_id = NULL)

Arguments

subscription_key	Subscription key for your Microsoft Genomics service. (Example = "04afabfc1af94c8285faec2f15e4e459") Go to Azure portal and open your Genomics account page. Under the 'Management' heading, choose 'Access keys'. There, you find both the API URL and your access keys.
region	Region of your Microsoft Genomics service. (Example = '"eastus"')
description	Description string for your submission. (Default = "Submission from msgen R package.")
process	Defines which pipeline to run. Either '"snapgatk"' (default) or '"gatk4"'.
reference	Process arguments for specifying a reference genome. Select from '"b37m1"', '"hg38m1"', '"hg38m1x"', or '"hg19m1"' (default).
input_storage_account_name	Azure storage account name where input files reside.
input_storage_account_key	Azure storage account key which will be used to create temporary access tokens for input files.
input_container_name	Azure blob container where input files reside.
blob_name_1	First file name.
blob_name_2	Second file name, needed only if input is in the FASTQ format.
output_storage_account_name	Azure storage account name where output files will be placed. (Optional: Will default to input storage account if not specified.)
output_storage_account_key	Azure storage account key which will be used to create a temporary access token for an output container. (Optional: Will default to input key if not specified.)
output_container_name	Azure blob container where output files will be placed. (Optional: Will default to input container if not specified.)
workflow_id	Workflow ID returned after submitting a job.

Examples

submit_workflow(subscription_key = "04afabfc...",
       region = "eastus",
       process = "snapgatk",
       reference = "b37m1",
       input_storage_account_name = "mygenomicsstorage",
       input_storage_account_key= "6GyBAbvgw5sqo2...",
       input_container_name = "myinputdata",
       blob_name_1 = "NA12878-chr21_1.fq.gz",
       blob_name_2 = "NA12878-chr21_2.fq.gz")
       
list_workflows(subscription_key = "04afabfc...",
     region = "eastus")
     
get_workflow_status(subscription_key = "04afabfc...",
       region = "eastus",
       workflow_id = "12g3c5a...")

cancel_workflow(subscription_key = "04afabfc...",
       region = "eastus",
       workflow_id = "12g3c5a...")

colbyford/msgen documentation built on May 9, 2021, 2:52 p.m.