Mercurial > repos > mini > strelka

comparison strelka_wrapper.py @ 8:2cee4ed50058

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
nothing relevant
author mini
date Fri, 26 Sep 2014 14:33:07 +0200
parents 3e8541ece3c7
children 0e8e6011082b f66f23fcc83a
comparison
equal deleted inserted replaced
7:3e8541ece3c7 8:2cee4ed50058
91 parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False ) 91 parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False )
92 parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False ) 92 parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False )
93 parser.add_argument( '--scriptPath', help='path to tumor bam file', required = False ) 93 parser.add_argument( '--scriptPath', help='path to tumor bam file', required = False )
94 args = parser.parse_args() 94 args = parser.parse_args()
95 95
96 root_dir= SCRIPT_PATH 96 root_dir= args.scriptPath
97 expected_dir="for_tests" 97 expected_dir="for_tests"
98 job_dir=os.getcwd() 98 job_dir=os.getcwd()
99 analysis_dir=job_dir + "/StrelkaAnalysis" 99 analysis_dir=job_dir + "/StrelkaAnalysis"
100 config_script=root_dir + "/configureStrelkaWorkflow.pl" 100 config_script=root_dir + "/configureStrelkaWorkflow.pl"
101 tmp_dir = "tmp" #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' ) 101 tmp_dir = "tmp" #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )