Merge pull request #297 from vsmalladi/azure

Add in template for Azure Workflow

.github/workflows/main.yml

@@ -21,6 +21,7 @@ jobs:
             - 'alice'
             - 'aws_tower'
             - 'awsbatch'
+            - 'azurebatch'
             - 'bi'
             - 'bigpurple'
             - 'binac'

README.md

@@ -88,6 +88,7 @@ Currently documentation is available for the following systems:
 * [ALICE](docs/alice.md)
 * [AWSBATCH](docs/awsbatch.md)
 * [AWS_TOWER](docs/aws_tower.md)
+* [AZUREBATCH](docs/azurebatch.md)
 * [BIGPURPLE](docs/bigpurple.md)
 * [BI](docs/bi.md)
 * [BINAC](docs/binac.md)

conf/azurebatch.config

@@ -0,0 +1,25 @@
+//Nextflow config file for running on Azure batch
+params {
+  config_profile_description = 'AWSBATCH Cloud Profile'
+  config_profile_contact = 'Venkat Malladi (@vsmalladi)'
+  config_profile_url = 'https://azure.microsoft.com/services/batch/'
+
+  az_location = 'westus2'
+  batch_name = false
+  batch_key = false
+  storage_name = false
+  sas_token = false
+}
+
+docker {
+  enabled = true
+}
+
+
+azure.batch.location = params.az_location
+azure.batch.accountName = params.batch_name
+azure.batch.accountKey = params.batch_key
+azure.batch.autoPoolMode = true
+azure.storage.accountName = params.storage_name
+azure.storage.sasToken = params.sas_token
+process.executor = 'azurebatch'

docs/azurebatch.md

@@ -0,0 +1,34 @@
+# nf-core/configs: azurebatch Configuration
+
+To be used with the `azurebatch` profile by specifying the `-profile azurebatch` when running nf-core pipelines.
+Custom queue and storage need to be supplied with `params.az_location`, `params.batch_name`, `params.batch_key`, `params.storage_name`, `params.sas_token`.
+
+## Required Parameters
+
+### `--az_location`
+
+The Azure Batch region where the computation is executed in VMs. Default (`westus2`).
+
+### `--batch_name`
+
+The Azure Batch account name.
+
+### `--batch_key`
+
+The Azure Batch account key.
+
+### `--storage_name`
+
+The Azure Blob Storage name. Example is currently [Illumina Platinum Genomes](https://docs.microsoft.com/en-us/azure/open-datasets/dataset-illumina-platinum-genomes?tabs=azure-storage). **This must be changed to your specific storage account.**
+
+### `--sas_token`
+
+The Azure Blob Storage shared access signature token.  Example is currently [Illumina Platinum Genomes](https://docs.microsoft.com/en-us/azure/open-datasets/dataset-illumina-platinum-genomes?tabs=azure-storage). **This must be changed to your specific storage account.**
+
+### `-w`
+
+The Azure Blob container to be used as Nextflow work directory (`-w az://work`).
+
+## Azure Batch Setup
+
+Please refer to the [Nextflow](https://www.nextflow.io/docs/edge/azure.html) documentation which describe how to setup the Azure Batch environment.

nfcore_custom.config

@@ -14,6 +14,7 @@ profiles {
   alice        { includeConfig "${params.custom_config_base}/conf/alice.config" }
   aws_tower    { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
+  azurebatch   { includeConfig "${params.custom_config_base}/conf/azurebatch.config" }
   bi           { includeConfig "${params.custom_config_base}/conf/bi.config" }
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
@@ -40,7 +41,7 @@ profiles {
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
-  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
+  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }