addressed changes in the last review

broadinstitute · Jan 5, 2024 · 47c3da3 · 47c3da3
1 parent a1bb4fe
commit 47c3da3
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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 ""}