def _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir): utils.safe_makedir(tx_work_dir) cmd = [sys.executable, os.path.realpath(utils.which("configureStrelkaGermlineWorkflow.py"))] cmd += ["--referenceFasta=%s" % ref_file, "--callRegions=%s" % get_region_bed(region, items, out_file), "--ploidy=%s" % _get_ploidy(shared.to_multiregion(region), items, out_file), "--runDir=%s" % tx_work_dir] cmd += ["--bam=%s" % b for b in align_bams] if any(dd.get_coverage_interval(d) not in ["genome"] for d in items): cmd += ["--targeted"] do.run(cmd, "Configure Strelka2 germline calling: %s" % (", ".join([dd.get_sample_name(d) for d in items]))) return os.path.join(tx_work_dir, "runWorkflow.py")
def _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir): utils.safe_makedir(tx_work_dir) cmd = [sys.executable, os.path.realpath(utils.which("configureStrelkaGermlineWorkflow.py"))] cmd += ["--referenceFasta=%s" % ref_file, "--callRegions=%s" % _get_region_bed(region, items, out_file), "--ploidy=%s" % _get_ploidy(shared.to_multiregion(region), items, out_file), "--runDir=%s" % tx_work_dir] cmd += ["--bam=%s" % b for b in align_bams] if any(dd.get_coverage_interval(d) not in ["genome"] for d in items): cmd += ["--targeted"] do.run(cmd, "Configure Strelka2 germline calling: %s" % (", ".join([dd.get_sample_name(d) for d in items]))) return os.path.join(tx_work_dir, "runWorkflow.py")
def _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir): utils.safe_makedir(tx_work_dir) cmd = [utils.get_program_python("configureStrelkaGermlineWorkflow.py"), os.path.realpath(utils.which("configureStrelkaGermlineWorkflow.py"))] cur_bed = get_region_bed(region, items, out_file) cmd += ["--referenceFasta=%s" % ref_file, "--callRegions=%s" % cur_bed, "--ploidy=%s" % _get_ploidy(shared.to_multiregion(region), items, out_file), "--runDir=%s" % tx_work_dir] cmd += ["--bam=%s" % b for b in align_bams] if _is_targeted_region(cur_bed, items[0]): cmd += ["--targeted"] do.run(cmd, "Configure Strelka2 germline calling: %s" % (", ".join([dd.get_sample_name(d) for d in items]))) return os.path.join(tx_work_dir, "runWorkflow.py")