diff --git a/src/sv-pipeline/04_variant_resolution/scripts/split_variants.py b/src/sv-pipeline/04_variant_resolution/scripts/split_variants.py index 118d8c83f..34e36dba9 100644 --- a/src/sv-pipeline/04_variant_resolution/scripts/split_variants.py +++ b/src/sv-pipeline/04_variant_resolution/scripts/split_variants.py @@ -78,7 +78,7 @@ def main(): parser = argparse.ArgumentParser() parser.add_argument("--bed", help="Path to input bed file", required=True) parser.add_argument("--n", help="number of variants per file", required=True) - parser.add_argument("--bca", default=False, help="If there are bcas to address set to True", action='store_true') + parser.add_argument("--bca", default=False, help="Flag to set to True if the VCF contains BCAs", action='store_true') parser.add_argument("--log-level", required=False, default="INFO", help="Specify level of logging information") args = parser.parse_args() diff --git a/wdl/TasksGenotypeBatch.wdl b/wdl/TasksGenotypeBatch.wdl index 37a86993b..4e0d44021 100644 --- a/wdl/TasksGenotypeBatch.wdl +++ b/wdl/TasksGenotypeBatch.wdl @@ -31,7 +31,7 @@ task SplitVariants { set -euo pipefail svtk vcf2bed ~{vcf} bed_file.bed python /opt/sv-pipeline/04_variant_resolution/scripts/split_variants.py \ - --bed bed_file.bed \ + --bed bed_file.bed \ ~{"--n " + n_per_split} \ ~{if generate_bca then "--bca" else ""}