From 9ea22fe5e03808f219885e6bdd4746ae70e8da5e Mon Sep 17 00:00:00 2001
From: Mageshwaran Murugaian <mageshwaran@lifebit.ai>
Date: Mon, 29 May 2023 22:56:46 +0530
Subject: [PATCH 1/3] Add azure config

---
 conf/azurebatch.config | 42 ++++++++++++++++++++++++++++++++++++++++++
 nextflow.config        |  8 ++++----
 2 files changed, 46 insertions(+), 4 deletions(-)
 create mode 100644 conf/azurebatch.config

diff --git a/conf/azurebatch.config b/conf/azurebatch.config
new file mode 100644
index 0000000..699a840
--- /dev/null
+++ b/conf/azurebatch.config
@@ -0,0 +1,42 @@
+
+params {
+  executor = 'azurebatch'
+  dataLocation = 'az://lifebit.blob.core.windows.net/sample-c2/pipelines/spammer-nf/input_files'
+  batchAccountName = ''
+  region = 'ukwest'
+  tenantId = ''
+  servicePrincipalId = ''
+  servicePrincipalSecret = ''
+  vmType = '*'
+  maxVmCount = 2
+  diskType = 'standard_lrs'
+  diskSize = '100 GB'
+  spot = true
+}
+
+azure {
+    activeDirectory {
+        servicePrincipalId = params.servicePrincipalId
+        servicePrincipalSecret = params.servicePrincipalSecret
+        tenantId = params.tenantId
+    }
+
+  batch {
+    location = params.region
+    accountName = params.batchAccountName
+    deleteJobsOnCompletion = false
+    autoPoolMode = true
+    deletePoolsOnCompletion = true
+    pools {
+      auto {
+        autoScale = true
+        vmType = params.vmType
+        maxVmCount = params.maxVmCount
+        vmCount = 1
+        spot = params.spot
+        diskType = params.diskType
+        diskSize = params.diskSize
+      }
+    }
+  }
+}
diff --git a/nextflow.config b/nextflow.config
index 14250e8..8ef5d56 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -7,7 +7,7 @@ params {
 	processA_cpus = 1
 	processA_disk = '20.GB'
 	mainScript = 'main.nf'
-	config = 'conf/standard.config'
+	config = 'standard'
 	dataLocation = 's3://lifebit-featured-datasets/pipelines/spammer-nf/input_files'
 	fileSuffix = ''
 	repsProcessA = 2
@@ -56,7 +56,7 @@ params {
 // includeConfig params.config 
 // outside of profiles scope, it will fail to update the values of the params
 profiles {
-	standard {includeConfig params.config}
+	standard { includeConfig "conf/${params.config}.config" }
 }
 
 // Do not change order of block, must follow after profiles scope (last section that updates params)
@@ -69,8 +69,8 @@ process {
 
     withName: processA {
         disk = params.processA_disk
-	cpus = params.processA_cpus
-	memory = params.processA_memory
+        cpus = params.processA_cpus
+        memory = params.processA_memory
 	}
 }
 

From 79dacd30939e2158b028b92a706b183424a7dd21 Mon Sep 17 00:00:00 2001
From: Mageshwaran Murugaian <mageshwaran@lifebit.ai>
Date: Tue, 6 Jun 2023 11:34:10 +0530
Subject: [PATCH 2/3] Update vmType

---
 conf/azurebatch.config | 2 +-
 nextflow.config        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/azurebatch.config b/conf/azurebatch.config
index 699a840..c1fa2af 100644
--- a/conf/azurebatch.config
+++ b/conf/azurebatch.config
@@ -7,7 +7,7 @@ params {
   tenantId = ''
   servicePrincipalId = ''
   servicePrincipalSecret = ''
-  vmType = '*'
+  vmType = 'STANDARD_D2S_V3'
   maxVmCount = 2
   diskType = 'standard_lrs'
   diskSize = '100 GB'
diff --git a/nextflow.config b/nextflow.config
index 8ef5d56..24dfaa7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -7,7 +7,7 @@ params {
 	processA_cpus = 1
 	processA_disk = '20.GB'
 	mainScript = 'main.nf'
-	config = 'standard'
+	config = 'conf/standard.config'
 	dataLocation = 's3://lifebit-featured-datasets/pipelines/spammer-nf/input_files'
 	fileSuffix = ''
 	repsProcessA = 2
@@ -56,7 +56,7 @@ params {
 // includeConfig params.config 
 // outside of profiles scope, it will fail to update the values of the params
 profiles {
-	standard { includeConfig "conf/${params.config}.config" }
+	standard {includeConfig params.config}
 }
 
 // Do not change order of block, must follow after profiles scope (last section that updates params)

From 01e6cc82acf5ffc5b6f7b695bd9ca7609e9390e4 Mon Sep 17 00:00:00 2001
From: Mageshwaran Murugaian <mageshwaran@lifebit.ai>
Date: Tue, 6 Jun 2023 11:37:41 +0530
Subject: [PATCH 3/3] chore: revert azure path to s3 original path, will update
 once data moved to Azure

---
 conf/azurebatch.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/azurebatch.config b/conf/azurebatch.config
index c1fa2af..efdd324 100644
--- a/conf/azurebatch.config
+++ b/conf/azurebatch.config
@@ -1,7 +1,7 @@
 
 params {
   executor = 'azurebatch'
-  dataLocation = 'az://lifebit.blob.core.windows.net/sample-c2/pipelines/spammer-nf/input_files'
+  dataLocation = 's3://lifebit-featured-datasets/pipelines/spammer-nf/input_files'
   batchAccountName = ''
   region = 'ukwest'
   tenantId = ''