From ec4e0c7e52237d88ebf42de16b599fa591d03cae Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 9 Feb 2021 21:09:49 -0600
Subject: [PATCH] Add dnanexus configs

---
 workflow/conf/dnanexus.config | 91 +++++++++++++++++++++++++++++++++++
 workflow/nextflow.config      |  3 ++
 2 files changed, 94 insertions(+)
 create mode 100755 workflow/conf/dnanexus.config

diff --git a/workflow/conf/dnanexus.config b/workflow/conf/dnanexus.config
new file mode 100755
index 0000000..0dbcbaa
--- /dev/null
+++ b/workflow/conf/dnanexus.config
@@ -0,0 +1,91 @@
+params {
+  refSource = "prod"
+}
+
+process {
+  withName:trackStart {
+    executor = 'local'
+  }
+  withName:getBag {
+    executor = 'local'
+  }
+  withName:getData {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:parseMetadata {
+    executor = 'local'
+  }
+  withName:trimData {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:getRefInfer {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:downsampleData {
+    executor = 'local'
+  }
+  withName:alignSampleData {
+    machineType = 'mem3_ssd1_v2_x16'
+  }
+  withName:inferMetadata {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:checkMetadata {
+    executor = 'local'
+  }
+  withName:getRef {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:alignData {
+    queue = '256GB,256GBv1'
+  }
+  withName:dedupData {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:countData {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:makeBigWig {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:fastqc {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:dataQC {
+    machineType = 'mem1_ssd1_v2_x16'
+  }
+  withName:aggrQC {
+    executor = 'local'
+  }
+  withName:uploadInputBag {
+    executor = 'local'
+  }
+  withName:uploadExecutionRun {
+    executor = 'local'
+  }
+  withName:uploadQC {
+    executor = 'local'
+  }
+  withName:uploadProcessedFile {
+    executor = 'local'
+  }
+  withName:uploadOutputBag {
+    executor = 'local'
+  }
+  withName:finalizeExecutionRun {
+    executor = 'local'
+  }
+  withName:failPreExecutionRun {
+    executor = 'local'
+  }
+  withName:failExecutionRun {
+    executor = 'local'
+  }
+  withName:uploadQC_fail {
+    executor = 'local'
+  }
+}
+
+docker {
+  enabled = true
+}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 44f2df5..927e605 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -16,6 +16,9 @@ profiles {
     includeConfig 'conf/aws.config'
     includeConfig 'conf/spot.config'
   }
+  dnanexus {
+    includeConfig 'conf/dnanexus.config'
+  }
 }
 
 process {
-- 
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