# HG changeset patch
# User mini
# Date 1412163933 -7200
# Node ID 8260a4188b0843daa65a4df67bcdaa7a26df1d15
# Parent  024468e8638cea4112bb459e4c9a090aa0794355
solved conf_file.ini pb

diff -r 024468e8638c -r 8260a4188b08 strelka.xml
--- a/strelka.xml	Wed Oct 01 12:33:46 2014 +0200
+++ b/strelka.xml	Wed Oct 01 13:45:33 2014 +0200
@@ -113,7 +113,7 @@
     <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf">
       <filter>output4_file_check == True</filter>
     </data>
-    <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
+    <data format="tabular" name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/config.ini">
       <filter>conf_file_check == True</filter>
     </data>
     <data format="bam" name="output5_bam" label="${tool.name} on ${on_string}(normal.realigned.bam)" from_work_dir="StrelkaAnalysis/realigned/normal.realigned.bam">
diff -r 024468e8638c -r 8260a4188b08 strelka_wrapper.py
--- a/strelka_wrapper.py	Wed Oct 01 12:33:46 2014 +0200
+++ b/strelka_wrapper.py	Wed Oct 01 13:45:33 2014 +0200
@@ -58,6 +58,7 @@
 
 def __main__():
     #Manage options
+    print(os.environ['PATH'])
     parser = argparse.ArgumentParser()                                             
     parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
     parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )   
@@ -139,6 +140,10 @@
     print("**** workflow cmd: '" + cmd + "'")
     my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
     print("**** completed workflow execution")
+    
+    cmdbash="cp %s %s" % (config_ini, analysis_dir + "/config.ini")
+    my_Popen(cmdbash, "copy_final_conf_file_err", tmp_dir, "Error during the copy of conf file after job is done, quite strange...")  
+
 
 if __name__=='__main__':
     __main__()