def main():
args = parse_args()
if args["which"] == "generate_config":
generate_config(args)
return
if args["which"] == "clean_sentinels":
clean_sentinels(args)
return
if args["run_with_docker"]:
run_with_docker(args, sys.argv)
return
if args["which"] == "alignment":
alignment_pipeline(args)
if args["which"] == "hmmcopy":
hmmcopy_pipeline(args)
if args["which"] == "annotation":
annotation_pipeline(args)
if args["which"] == "merge_cell_bams":
merge_bams_pipeline(args)
if args["which"] == "split_wgs_bam":
split_bam_pipeline(args)
if args["which"] == "variant_calling":
variant_calling_pipeline(args)
if args["which"] == "germline_calling":
germline_calling_pipeline(args)
if args["which"] == "infer_haps":
infer_haps_pipeline(args)
if args["which"] == "count_haps":
count_haps_pipeline(args)
if args["which"] == "breakpoint_calling":
breakpoint_calling_pipeline(args)
if args["which"] == "snv_genotyping":
snv_genotyping_pipeline(args)
if args["which"] == "sv_genotyping":
sv_genotyping_pipeline(args)
if args["which"] == "pseudo_bulk_qc":
pseudo_bulk_qc_pipeline(args)
def main():
args = parse_args()
if args["which"] == "generate_config":
generate_config(args)
return
if args["which"] == "clean_sentinels":
clean_sentinels(args)
return
if args["run_with_docker"]:
run_with_docker(args, sys.argv)
return
if args["which"] == "qc":
qc_pipeline(args)
if args["which"] == "aneufinder":
aneufinder_pipeline(args)
if args["which"] == "merge_bams":
merge_bams_pipeline(args)
if args["which"] == "split_bam":
split_bam_pipeline(args)
if args["which"] == "variant_calling":
variant_calling_pipeline(args)
if args["which"] == "copy_number_calling":
copy_number_calling_pipeline(args)
if args["which"] == "infer_haps":
infer_haps_pipeline(args)
if args["which"] == "germline_calling":
germline_calling_pipeline(args)
if args["which"] == "breakpoint_calling":
breakpoint_calling_pipeline(args)
if args["which"] == "variant_counting":
variant_counting_pipeline(args)
if args["which"] == "ltm":
ltm_pipeline(args)
if args["which"] == "multi_sample_pseudo_bulk":
multi_sample_pipeline(args)