From 845a9ce971997fe1b3f858b0e894d97e4a45892b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <vmalladi@microsoft.com>
Date: Thu, 18 Nov 2021 15:47:27 -0600
Subject: [PATCH] Update Readme with more inforamtion on the options.

---
 conf/azurebatch.config |  5 +++--
 docs/azurebatch.md     | 28 ++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+), 2 deletions(-)

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.