diff --git a/Makefile b/Makefile
index 997cfaa..7e37ffe 100644
--- a/Makefile
+++ b/Makefile
@@ -2,4 +2,4 @@ init:
 	pip install -r requirements.txt
 
 test:
-	nosetests tests
+	nosetests -v --with-coverage --cover-tests tests
diff --git a/mutect/filter_mutect.py b/mutect/filter_mutect.py
index 45ce708..bce04dd 100644
--- a/mutect/filter_mutect.py
+++ b/mutect/filter_mutect.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
 '''
 @Description : This tool helps to filter muTect v1.14 txt and vcf through command line. 
 @Created :  07/17/2016
diff --git a/mutect/outputs.yaml b/mutect/outputs.yaml
index 1450337..25ca859 100644
--- a/mutect/outputs.yaml
+++ b/mutect/outputs.yaml
@@ -16,4 +16,4 @@ outputs:
           if (inputs.inputTxt)
             return inputs.inputTxt.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
           return null;
-        }
\ No newline at end of file
+        }
diff --git a/mutect/postprocess.py b/mutect/postprocess.py
index cb68bf3..5e64dd6 100755
--- a/mutect/postprocess.py
+++ b/mutect/postprocess.py
@@ -3,7 +3,7 @@
 
 import argparse
 import ruamel.yaml
-
+import os
 
 def read(filename):
     """return file contents"""
@@ -33,14 +33,14 @@ def main():
     )
 
     params = parser.parse_args()
-
+    dir_path = os.path.dirname(os.path.realpath(__file__))
     cwl = ruamel.yaml.load(read(params.filename_cwl),
                            ruamel.yaml.RoundTripLoader)
-
+    script_path = os.path.join(dir_path,'filter_mutect.py')
+    cwl['baseCommand'] = ['python',script_path]
     cwl['inputs']['inputVcf']['type'] = ['string', 'File']
     cwl['inputs']['inputTxt']['type'] = ['string', 'File']
-    cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
-    cwl['inputs']['version']['default'] = 'default'
+    cwl['inputs']['hotspotVcf']['type'] = ['null','string', 'File']
 
     write(params.filename_cwl, ruamel.yaml.dump(
         cwl, Dumper=ruamel.yaml.RoundTripDumper))
diff --git a/pindel/filter_pindel.py b/pindel/filter_pindel.py
index 5c7c3c3..10ab0c9 100644
--- a/pindel/filter_pindel.py
+++ b/pindel/filter_pindel.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
 """
 @Description : This tool helps to filter pindel v0.2.5a7 vcf through command line. 
 @Created :  07/17/2014
diff --git a/pindel/outputs.yaml b/pindel/outputs.yaml
index 9d311f9..783b575 100644
--- a/pindel/outputs.yaml
+++ b/pindel/outputs.yaml
@@ -16,4 +16,4 @@ outputs:
           if (inputs.inputVcf)
             return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
           return null;
-        }
\ No newline at end of file
+        }
diff --git a/pindel/postprocess.py b/pindel/postprocess.py
index f5aebd3..3b308e0 100755
--- a/pindel/postprocess.py
+++ b/pindel/postprocess.py
@@ -3,7 +3,7 @@
 
 import argparse
 import ruamel.yaml
-
+import os
 
 def read(filename):
     """return file contents"""
@@ -33,13 +33,15 @@ def main():
     )
 
     params = parser.parse_args()
-
+    dir_path = os.path.dirname(os.path.realpath(__file__))
     cwl = ruamel.yaml.load(read(params.filename_cwl),
                            ruamel.yaml.RoundTripLoader)
 
+    script_path = os.path.join(dir_path,'filter_pindel.py')
+    cwl['baseCommand'] = ['python',script_path]
     cwl['inputs']['inputVcf']['type'] = ['string', 'File']
-    cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
-    cwl['inputs']['version']['default'] = 'default'
+    cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']
+    
 
     write(params.filename_cwl, ruamel.yaml.dump(
         cwl, Dumper=ruamel.yaml.RoundTripDumper))
diff --git a/setup.py b/setup.py
index 8b77c4e..e62395e 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name='basicfiltering',
-    version='0.1.0',
+    version='0.1.3',
     description='Package for filtering multiple variant calling tools',
     long_description=readme,
     author='Ronak Shah',
diff --git a/somaticindeldetector/filter_sid.py b/somaticindeldetector/filter_sid.py
index 25bfe88..afbaed9 100644
--- a/somaticindeldetector/filter_sid.py
+++ b/somaticindeldetector/filter_sid.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
 '''
 @Description : This tool helps to filter SomaticIndelDetector vcf and txt through command line.GATK version: 2.3-9
 @Created :  07/25/2016
diff --git a/somaticindeldetector/outputs.yaml b/somaticindeldetector/outputs.yaml
index 9d311f9..783b575 100644
--- a/somaticindeldetector/outputs.yaml
+++ b/somaticindeldetector/outputs.yaml
@@ -16,4 +16,4 @@ outputs:
           if (inputs.inputVcf)
             return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
           return null;
-        }
\ No newline at end of file
+        }
diff --git a/somaticindeldetector/postprocess.py b/somaticindeldetector/postprocess.py
index cb68bf3..306d1b9 100755
--- a/somaticindeldetector/postprocess.py
+++ b/somaticindeldetector/postprocess.py
@@ -3,7 +3,7 @@
 
 import argparse
 import ruamel.yaml
-
+import os
 
 def read(filename):
     """return file contents"""
@@ -33,14 +33,15 @@ def main():
     )
 
     params = parser.parse_args()
-
+    dir_path = os.path.dirname(os.path.realpath(__file__))
     cwl = ruamel.yaml.load(read(params.filename_cwl),
                            ruamel.yaml.RoundTripLoader)
 
+    script_path = os.path.join(dir_path,'filter_sid.py')
+    cwl['baseCommand'] = ['python',script_path]
     cwl['inputs']['inputVcf']['type'] = ['string', 'File']
     cwl['inputs']['inputTxt']['type'] = ['string', 'File']
-    cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
-    cwl['inputs']['version']['default'] = 'default'
+    cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']
 
     write(params.filename_cwl, ruamel.yaml.dump(
         cwl, Dumper=ruamel.yaml.RoundTripDumper))
diff --git a/vardict/filter_vardict.py b/vardict/filter_vardict.py
index aa9c8fd..7564537 100644
--- a/vardict/filter_vardict.py
+++ b/vardict/filter_vardict.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
 '''
 @Description : This tool helps to filter vardict vcf through command line for version 1.4.6
 @Created :  04/22/2016
diff --git a/vardict/outputs.yaml b/vardict/outputs.yaml
index 9d311f9..783b575 100644
--- a/vardict/outputs.yaml
+++ b/vardict/outputs.yaml
@@ -16,4 +16,4 @@ outputs:
           if (inputs.inputVcf)
             return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
           return null;
-        }
\ No newline at end of file
+        }
diff --git a/vardict/postprocess.py b/vardict/postprocess.py
index f5aebd3..7da8611 100755
--- a/vardict/postprocess.py
+++ b/vardict/postprocess.py
@@ -3,7 +3,7 @@
 
 import argparse
 import ruamel.yaml
-
+import os
 
 def read(filename):
     """return file contents"""
@@ -33,13 +33,14 @@ def main():
     )
 
     params = parser.parse_args()
-
+    dir_path = os.path.dirname(os.path.realpath(__file__))
     cwl = ruamel.yaml.load(read(params.filename_cwl),
                            ruamel.yaml.RoundTripLoader)
 
+    script_path = os.path.join(dir_path,'filter_vardict.py')
+    cwl['baseCommand'] = ['python',script_path]
     cwl['inputs']['inputVcf']['type'] = ['string', 'File']
-    cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
-    cwl['inputs']['version']['default'] = 'default'
+    cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']
 
     write(params.filename_cwl, ruamel.yaml.dump(
         cwl, Dumper=ruamel.yaml.RoundTripDumper))