From 3d3a2c756d0ed29bc94c749b94a3319d68221226 Mon Sep 17 00:00:00 2001 From: boasvdp <boasvdp@gmail.com> Date: Fri, 26 Apr 2024 10:41:25 +0200 Subject: [PATCH] style: black formatting --- assembly_snptyper/main.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/assembly_snptyper/main.py b/assembly_snptyper/main.py index afbaf65..5439f5d 100644 --- a/assembly_snptyper/main.py +++ b/assembly_snptyper/main.py @@ -63,6 +63,7 @@ def check_if_ref_is_ascii(reference): "Reference genome cannot be read as flat text: only unzipped FASTA reference genomes are supported." ) + def convert_vcf_to_bed(vcf, bed_path): """ Convert reference VCF to BED file @@ -264,7 +265,10 @@ def wrapper(args_dict): """ sample = Path(args_dict["input_asm"]).stem result = run_oneliner( - args_dict["bed_path"], args_dict["reference"], args_dict["input_asm"], args_dict["minimap_preset"] + args_dict["bed_path"], + args_dict["reference"], + args_dict["input_asm"], + args_dict["minimap_preset"], ) output = parse_mpileup_output(result, args_dict["vcf"], sample) logging.info(f"Processed {sample}") @@ -404,7 +408,9 @@ def main(): logging.info(f"Created temporary bed file: {bed_path}") logging.info("Starting typing workflow") - run_parallel(bed_path, args.reference, list_input, args.vcf, minimap_preset, args.processes) + run_parallel( + bed_path, args.reference, list_input, args.vcf, minimap_preset, args.processes + ) if __name__ == "__main__":