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")
