output ped from ValidatePedFile to enforce order of execution

broadinstitute · Aug 17, 2023 · 04c8384 · 04c8384
1 parent 6dab052
commit 04c8384
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/wdl/GatherBatchEvidence.wdl b/wdl/GatherBatchEvidence.wdl
@@ -225,7 +225,7 @@ workflow GatherBatchEvidence {
 
   call util.SubsetPedFile {
     input:
-      ped_file = ped_file,
+      ped_file = ValidatePedFile.output_ped,
       sample_list = write_lines(samples_batch),
       subset_name = batch,
       sv_base_mini_docker = sv_base_mini_docker,

diff --git a/wdl/Utils.wdl b/wdl/Utils.wdl
@@ -422,10 +422,13 @@ task ValidatePedFile {
 
     set -euo pipefail
     python opt/sv-pipeline/scripts/validate_ped.py -p ~{ped_file} -s {sample_list}
-    # no outputs - task will either succeed or fail with details in log file
 
   >>>
 
+  output {
+    File output_ped = ped_file
+  }
+
   runtime {
     cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
     memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"