Mercurial > repos > mini > strelka
comparison strelka_wrapper.py @ 8:2cee4ed50058
nothing relevant
| author | mini |
|---|---|
| date | Fri, 26 Sep 2014 14:33:07 +0200 |
| parents | 3e8541ece3c7 |
| children | 0e8e6011082b f66f23fcc83a |
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| 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-' ) |