Deploy a Nextflow genomics cluster

Last updated: 14/06/2018

This template deploys a scalable Nextflow cluster with a Jumpbox, n cluster nodes, docker support and shared storage.

This Azure Resource Manager (ARM) template was created by a member of the community and not by Microsoft. Each ARM template is licensed to you under a licence agreement by its owner, not Microsoft. Microsoft is not responsible for ARM templates provided and licensed by community members and does not screen for security, compatibility or performance. Community ARM templates are not supported under any Microsoft support programme or service, and are made available AS IS without warranty of any kind.

Parameters

Parameter Name Description
dnsNameForJumpBox Unique DNS Name for the Public IP used to access the Docker Virtual Machine (master node).
vmImageReference The image to use for VMs created. This can be marketplace or custom image
vmNodeSku Size of VMs in the VM Scale Set.
vmMasterSku Size of VMs in the VM Scale Set.
vmMasterDiskType Choose between a standard disk for and SSD disk for the master nodes NFS fileshare
vmMasterDiskSize The SSD Size to be used for the NFS file share. For pricing details see https://azure.microsoft.com/en-us/pricing/details/managed-disks/
vmAdditionalInstallScriptUrl An additional installs script (bash run as root) to be run after nodes/master are configured. Can be used to mount additional storage or do additional setup
vmAdditionalInstallScriptArgument An argument to be passed to the additional install script
nextflowInstallUrl The install url for nextflow, this can be used to pin nextflow versions
instanceCount Number of cluster VM instances (100 or less).
adminUsername Admin username on all VMs.
adminPassword Admin password on all VMs.
vnetName Name of the virtual network to deploy the scale set into.
subnetName Name of the subnet to deploy the scale set into.
shareName Azure file share name.
mountpointPath Path on VM to mount file shares. '/datadisks/disk1/' is a Premium Managed disk with high iops, this will suit most uses.
nodeMaxCpus Sets the cluster.maxCpus setting on all cluster nodes
_artifactsLocation *Advanced* This is best left as default unless you are an advanced user. The base URI where artifacts required by this template are located.
_artifactsLocationSasToken *Advanced* This should be left as default unless you are an advanced user. The sasToken required to access _artifactsLocation. When the template is deployed using the accompanying scripts, a sasToken will be automatically generated.
_artifactsSharedFolder *Advanced* This should be left as default unless you are an advanced user. The folder in the artifacts location were shared scripts are stored.
_artifactsNextflowFolder *Advanced* This should be left as default unless you are an advanced user. The folder in teh artifacts location were nextflow scripts are stored.

Use the template

PowerShell

New-AzureRmResourceGroupDeployment -Name <deployment-name> -ResourceGroupName <resource-group-name> -TemplateUri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
Installing and configuring Azure PowerShell

Command line

azure config mode arm
azure group deployment create <my-resource-group> <my-deployment-name> --template-uri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/nextflow-genomics-cluster-ubuntu/azuredeploy.json
Installing and configuring the Azure cross-platform command-line interface