attempt to maybe fix the issue

broadinstitute · Feb 19, 2025 · 535c777 · 535c777
1 parent f822fee
commit 535c777
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/wdl/tasks/Z_One_Off_Analyses/BroadOnPremMalariaPipelineTasks.wdl b/wdl/tasks/Z_One_Off_Analyses/BroadOnPremMalariaPipelineTasks.wdl
@@ -160,13 +160,14 @@ task SortCompressIndexVcf {
 
         ################################
 
-        bcftools sort -m$((tot_mem_mb-2048))M -Oz2 -o ~{input_vcf}.gz ~{input_vcf}
-        bcftools index --threads ${np} --tbi  ~{input_vcf}.gz
+        # Ensure the output files are placed in the root execution directory (.)
+        bcftools sort -m$((tot_mem_mb-2048))M -Oz -o ./$(basename ~{input_vcf}).gz ~{input_vcf}
+        bcftools index --threads ${np} --tbi ./$(basename ~{input_vcf}).gz
     >>>
 
     output {
-        File vcf = "~{input_vcf}.gz"
-        File vcf_index = "~{input_vcf}.gz.tbi"
+        File sorted_vcf = "$(basename input_vcf).gz"
+        File sorted_vcf_index = "$(basename input_vcf).gz.tbi"
     }
 
     #########################