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Update Readme with more inforamtion on the options.

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Venkat Malladi 2021-11-18 15:47:27 -06:00
parent 219244f1b4
commit 845a9ce971
2 changed files with 31 additions and 2 deletions
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5
conf/azurebatch.config
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@ -7,8 +7,9 @@ params {
az_location = 'westus2' az_location = 'westus2'
batch_name = false batch_name = false
batch_key = false batch_key = false
storage_name = 'datasetplatinumgenomes' storage_name = 'platinumgenomes'
sas_token = 'sv=2019-02-02&se=2050-01-01T08%3A00%3A00Z&si=prod&sr=c&sig=FFfZ0QaDcnEPQmWsshtpoYOjbzd4jtwIWeK%2Fc4i9MqM%3D' sas_token = 'sv=2019-02-02&se=2050-01-01T08%3A00%3A00Z&si=prod&sr=c&sig=FFfZ0QaDcnEPQmWsshtpoYOjbzd4jtwIWeK%2Fc4i9MqM%3D'
work_dir = false
} }
docker { docker {
@ -22,5 +23,5 @@ azure.batch.accountKey = params.batch_key
azure.batch.autoPoolMode = true azure.batch.autoPoolMode = true
azure.storage.accountName = params.storage_name azure.storage.accountName = params.storage_name
azure.storage.sasToken = params.sas_token azure.storage.sasToken = params.sas_token
workDir = 'az://work'
process.executor = 'azurebatch' process.executor = 'azurebatch'
workDir = param.work_dir

28
docs/azurebatch.md
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@ -3,6 +3,34 @@
To be used with the `azurebatch` profile by specifying the `-profile azurebatch` when running nf-core pipelines. 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`. 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.**
### Optional Parameters
#### `--work_dir`
The Azure Blob container to be used as Nextflow work directory. Can also be specified with (`-w az://work`).
## Azure Batch Setup ## 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. Please refer to the [Nextflow](https://www.nextflow.io/docs/edge/azure.html) documentation which describe how to setup the Azure Batch environment.