made edits based on second review.

broadinstitute · Dec 22, 2023 · a1bb4fe · a1bb4fe
1 parent c590e1e
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diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -13,7 +13,7 @@
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2023-07-28-v0.28.1-beta-e70dfbd7",
   "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/vjalili/sv-base-mini:5994670",
   "sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
-  "sv_pipeline_docker": "us.gcr.io/talkowski-sv-gnomad/kveerara/sv-pipeline:kv_split_variants_8d7ca52",
+  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
   "sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
   "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",
   "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3",

diff --git a/wdl/TasksGenotypeBatch.wdl b/wdl/TasksGenotypeBatch.wdl
@@ -32,8 +32,8 @@ task SplitVariants {
     svtk vcf2bed ~{vcf} bed_file.bed
     python /opt/sv-pipeline/04_variant_resolution/scripts/split_variants.py \
     --bed bed_file.bed \
-    ~{"--n " + n_per_split} \
-    ~{if generate_bca then "--bca" else ""}
+      ~{"--n " + n_per_split} \
+      ~{if generate_bca then "--bca" else ""}
 
   >>>
   runtime {