Mercurial > repos > mini > strelka
changeset 17:8260a4188b08
solved conf_file.ini pb
| author | mini |
|---|---|
| date | Wed, 01 Oct 2014 13:45:33 +0200 |
| parents | 024468e8638c |
| children | 3c10d88b55ad |
| files | strelka.xml strelka_wrapper.py |
| diffstat | 2 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- 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">
--- 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__()