From b792e197436fe48d2ceb24c287d1156affefaa71 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Wed, 13 Sep 2017 11:22:20 -0400
Subject: [PATCH 1/3] bwa-mem cwl structure changed

---
 cwl_awsem/bwa-mem.cwl | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/cwl_awsem/bwa-mem.cwl b/cwl_awsem/bwa-mem.cwl
index 9dab614..d72e684 100644
--- a/cwl_awsem/bwa-mem.cwl
+++ b/cwl_awsem/bwa-mem.cwl
@@ -1,7 +1,7 @@
 {
     "hints": [
         {
-            "dockerPull": "duplexa/4dn-hic:v36",
+            "dockerPull": "duplexa/4dn-hic:v39",
             "class": "DockerRequirement"
         }
     ],
@@ -44,7 +44,7 @@
             ],
             "id": "#nThreads",
             "inputBinding": {
-                "position": 5,
+                "position": 6,
                 "separate": true
             },
             "default": 4
@@ -56,10 +56,22 @@
             ],
             "id": "#prefix",
             "inputBinding": {
-                "position": 4,
+                "position": 5,
                 "separate": true
             },
             "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "."
         }
     ],
     "outputs": [

From 5686b083a039085b7ef13094b455e40d1af78f77 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Wed, 13 Sep 2017 13:17:07 -0400
Subject: [PATCH 2/3] updated bwa benchmark

---
 Benchmark/Benchmark.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Benchmark/Benchmark.py b/Benchmark/Benchmark.py
index 92b72fd..e376238 100644
--- a/Benchmark/Benchmark.py
+++ b/Benchmark/Benchmark.py
@@ -93,7 +93,9 @@ def bwa_mem(input_json):
     total_input_size = data_input_size + input_sizes.get('bwa_index')
     output_bam_size = data_input_size * 1.5
     intermediate_index_size = input_sizes.get('bwa_index') * 2
-    total_intermediate_size = intermediate_index_size + output_bam_size
+    copied_input_size = data_input_size * 5  # copied and unzipped
+    total_intermediate_size \
+        = intermediate_index_size + output_bam_size + copied_input_size
     total_output_size = output_bam_size
     additional_size_in_gb = 4.5
 

From 1cc71defad29695a68ca6239034acc325b327ac8 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Wed, 13 Sep 2017 13:19:09 -0400
Subject: [PATCH 3/3] updated readme

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index ada78db..2f4f526 100644
--- a/README.md
+++ b/README.md
@@ -33,14 +33,14 @@ B.benchmark(app_name, input_json)
 * bwa-mem
 ```python
 app_name = 'bwa-mem'
-input_json = {'input_size_in_bytes': {'fastq1':93520,
-                                      'fastq2':97604,
-                                      'bwa_index':3364568},
+input_json = {'input_size_in_bytes': {'fastq1':93520000,
+                                      'fastq2':97604000,
+                                      'bwa_index':3364568000},
               'parameters': {'nThreads': 4}}
 B.benchmark(app_name, input_json)
 ```
 ```
-{'recommended_instance_type': 'c4.8xlarge', 'EBS_optimized': True, 'cost_in_usd': 1.591, 'EBS_optimization_surcharge': 0.0, 'mem_in_gb': 60.0, 'cpu': 36}
+{'aws': {'cost_in_usd': 0.188, 'EBS_optimization_surcharge': None, 'EBS_optimized': False, 'cpu': 4, 'mem_in_gb': 16.0, 'recommended_instance_type': 't2.xlarge'}, 'total_mem_in_MB': 12834.808349609375, 'total_size_in_GB': 15.502477258443832, 'min_CPU': 4}
 ```
 
 To use Benchmark in from other places, install it as below.