From 237f91a3b78386c41202417c31332aeb1ac33d16 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <vmalladi@microsoft.com>
Date: Thu, 18 Nov 2021 14:51:39 -0600
Subject: [PATCH] Add in minmum config for azure.

---
 .github/workflows/main.yml |  1 +
 README.md                  |  1 +
 conf/azurebatch.config     | 26 ++++++++++++++++++++++++++
 docs/azurebatch.md         |  8 ++++++++
 nfcore_custom.config       |  3 ++-
 5 files changed, 38 insertions(+), 1 deletion(-)
 create mode 100644 conf/azurebatch.config
 create mode 100644 docs/azurebatch.md

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 382a0f7..56d27e8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,6 +21,7 @@ jobs:
             - 'alice'
             - 'aws_tower'
             - 'awsbatch'
+            - 'azurebatch'
             - 'bi'
             - 'bigpurple'
             - 'binac'
diff --git a/README.md b/README.md
index 293a9c9..2771c5d 100644
--- a/README.md
+++ b/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)
diff --git a/conf/azurebatch.config b/conf/azurebatch.config
new file mode 100644
index 0000000..809e5dd
--- /dev/null
+++ b/conf/azurebatch.config
@@ -0,0 +1,26 @@
+//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 = 'westeurope'
+  batch_name = false
+  batch_key = false
+  storage_name = false
+  storage_key = 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.accountKey = params.storage_key
+workDir = 'az://work'
+process.executor = 'azurebatch'
diff --git a/docs/azurebatch.md b/docs/azurebatch.md
new file mode 100644
index 0000000..a9222b9
--- /dev/null
+++ b/docs/azurebatch.md
@@ -0,0 +1,8 @@
+# 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.storage_key`.
+
+## 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.
diff --git a/nfcore_custom.config b/nfcore_custom.config
index b1047b8..3e4dc5a 100644
--- a/nfcore_custom.config
+++ b/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" }