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 |
|---|---|
| location | Location for all resources |
| 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 the master node. |
| vmMasterDiskType | Choose between a standard disk for and SSD disk for the master node's 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. |
| authenticationType | Type of authentication to use on the Virtual Machine. SSH key is recommended. |
| adminPasswordOrKey | SSH Key or password for the Virtual Machine. SSH key is recommended. |
| 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 |
| forceUpdateTag | Determines whether to run the custom script extension on a subsequent deployment. Use the defaultValue. |
| _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. |
| _diskInitScriptUri | *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 the artifacts location were nextflow scripts are stored. |
Use the template
PowerShell
New-AzResourceGroup -Name <resource-group-name> -Location <resource-group-location> #use this command when you need to create a new resource group for your deploymentInstall and configure Azure PowerShell
New-AzResourceGroupDeployment -ResourceGroupName <resource-group-name> -TemplateUri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/application-workloads/nextflow/nextflow-genomics-cluster-ubuntu/azuredeploy.json
Command line
az group create --name <resource-group-name> --location <resource-group-location> #use this command when you need to create a new resource group for your deploymentInstall and Configure the Azure Cross-Platform Command-Line Interface
az group deployment create --resource-group <my-resource-group> --template-uri https://raw.githubusercontent.com/Azure/azure-quickstart-templates/master/application-workloads/nextflow/nextflow-genomics-cluster-ubuntu/azuredeploy.json