diff --git a/conf/azurebatch.config b/conf/azurebatch.config index 12c516b..22659b7 100644 --- a/conf/azurebatch.config +++ b/conf/azurebatch.config @@ -7,8 +7,9 @@ params { az_location = 'westus2' batch_name = 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' + work_dir = false } docker { @@ -22,5 +23,5 @@ azure.batch.accountKey = params.batch_key azure.batch.autoPoolMode = true azure.storage.accountName = params.storage_name azure.storage.sasToken = params.sas_token -workDir = 'az://work' process.executor = 'azurebatch' +workDir = param.work_dir diff --git a/docs/azurebatch.md b/docs/azurebatch.md index 7992fb9..ecfb9c2 100644 --- a/docs/azurebatch.md +++ b/docs/azurebatch.md @@ -3,6 +3,34 @@ 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.** + +### 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 Please refer to the [Nextflow](https://www.nextflow.io/docs/edge/azure.html) documentation which describe how to setup the Azure Batch environment.