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Merge pull request #297 from vsmalladi/azure

Add in template for Azure Workflow
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Phil Ewels 2021-11-19 00:55:54 +01:00 committed by GitHub
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5 changed files with 63 additions and 1 deletions

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

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@ -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)

25
conf/azurebatch.config Normal file
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@ -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'

34
docs/azurebatch.md Normal file
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@ -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.

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@ -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" }