Merge pull request #466 from vsmalladi/sarek

Add in Ddv4 series config.

README.md

@@ -279,6 +279,7 @@ Currently documentation is available for the following pipelines within specific
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)
 - sarek
+  - [AZUREBATCH](docs/pipeline/sarek/azurebatch.md)
   - [EVA](docs/pipeline/sarek/eva.md)
   - [MUNIN](docs/pipeline/sarek/munin.md)
   - [UPPMAX](docs/pipeline/sarek/uppmax.md)

conf/pipeline/sarek/azurebatch_pools_Ddv4.config

@@ -0,0 +1,61 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    nf-core/sarek Nextflow config file for Azure Batch pools
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines several Azure Batch pools with virtual machines from Ddv4-series,
+    assigns pools to labels according to the requirements defined in base.config.
+    You might need to adjust vmCount and maxVmCount depending on your Batch account quotas.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile azurebatch
+            --input 'az://<Path to input file>' --outdir 'az://<Output directory>'
+            -w 'az://<Work directory>' [<Other pipeline parameters>]
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_description = 'Azure Batch Ddv4 pools profile'
+    config_profile_contact = ' Venkat Malladi (@vsmalladi) & Olesya Melnichenko (@olesya13)'
+    config_profile_url = 'https://azure.microsoft.com/services/batch/'
+}
+
+process {
+    queue = 'Standard_D8d_v4'
+    withLabel:process_low   {queue = 'Standard_D8d_v4'}
+    withLabel:process_medium {queue = 'Standard_D16d_v4'}
+    withLabel:process_high {queue = 'Standard_D32d_v4'}
+    withLabel:process_high_memory {queue = 'Standard_D64d_v4'}
+}
+
+azure {
+    batch {
+        autoPoolMode = false
+        allowPoolCreation = true
+        pools {
+            Standard_D8d_v4 {
+                autoScale = true
+                vmType = 'Standard_D8d_v4'
+                vmCount = 2
+                maxVmCount = 20
+            }
+            Standard_D16d_v4 {
+                autoScale = true
+                vmType = 'Standard_D16d_v4'
+                vmCount = 2
+                maxVmCount = 20
+            }
+            Standard_D32d_v4 {
+                autoScale = true
+                vmType = 'Standard_D32d_v4'
+                vmCount = 2
+                maxVmCount = 20
+            }
+            Standard_D64d_v4 {
+                autoScale = true
+                vmType = 'Standard_D64d_v4'
+                vmCount = 2
+                maxVmCount = 10
+            }
+        }
+    }
+}

docs/pipeline/sarek/azurebatch

@@ -0,0 +1,13 @@
+# nf-core/configs: azurebatch sarek specific configuration
+
+Specific configuration for [nf-co.re/sarek](https://nf-co.re/sarek) pipeline
+
+## Usage
+
+To use, run nextflow with the pipeline using `-profile azurebatch`.
+
+This will download and launch the rnaseq specific [`azurebatch_pools_Ddv4.config`](../../../conf/pipeline/sarek/azurebatch_pools_Ddv4.config) which has been pre-configured with a setup suitable for Azure Batch.
+
+Before the first use check your Azure Batch account quota for Ddv4 Series, adjust it if needed.
+
+Example: `nextflow run nf-core/sarek -profile azurebatch`

pipeline/sarek.config

@@ -9,6 +9,7 @@
     */
 
 profiles {
+    azurebatch { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/azurebatch_pools_Ddv4.config" }
     cfc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
     cfc_dev { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
     eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }