attempt to maybe fix the issue

wdl/tasks/Z_One_Off_Analyses/BroadOnPremMalariaPipelineTasks.wdl

@@ -159,15 +159,13 @@ task SortCompressIndexVcf {
         tot_mem_mb=$(free -m | grep '^Mem' | awk '{print $2}')
 
         ################################
-
-        # Ensure the output files are placed in the root execution directory (.)
-        bcftools sort -m$((tot_mem_mb-2048))M -Oz -o ./$(basename ~{input_vcf}).gz ~{input_vcf}
-        bcftools index --threads ${np} --tbi ./$(basename ~{input_vcf}).gz
+        bcftools sort -m$((tot_mem_mb-2048))M -Oz2 -o ./$(basename ~{input_vcf}).gz ~{input_vcf}
+        bcftools index --threads ${np} --tbi  ~$(basename ~{input_vcf}).gz
     >>>
 
     output {
-        File sorted_vcf = "$(basename input_vcf).gz"
-        File sorted_vcf_index = "$(basename input_vcf).gz.tbi"
+        File vcf = "$(basename ~{input_vcf}).gz"
+        File vcf_index = "$(basename ~{input_vcf}).gz.tbi"
     }
 
     #########################