bug fix

Author: VJalili

dockerfiles/all/Dockerfile

@@ -72,7 +72,9 @@ RUN /app/scramble-gatk-sv/cluster_identifier/src/build/cluster_identifier -v
 # define default command
 CMD ["Rscript"]
 
+FROM us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-10-25-v0.29-beta-5ea22a52
 
+# this layer must remain last
 FROM us.gcr.io/broad-dsde-methods/gatk-sv/gatk:2024-12-05-4.6.1.0-6-gfc248dfc1-NIGHTLY-SNAPSHOT
 
-FROM us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-10-25-v0.29-beta-5ea22a52
+WORKDIR /

src/bash_workflows/collect_counts.sh

@@ -18,7 +18,7 @@ command_mem_mb=10240
 
 declare -a disabled_read_filters_arr
 if [ -n "$disabled_read_filters" ]; then
-  disabled_read_filters_arr=( "--disable-read-filter ${disabled_read_filters}" )
+  disabled_read_filters_arr=( "--disable-read-filter" "${disabled_read_filters}" )
 else
   disabled_read_filters_arr=()
 fi