Output VaPoR header with # (#387)

broadinstitute · Aug 18, 2022 · ccceea0 · ccceea0
1 parent 9e32e40
commit ccceea0
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -22,7 +22,7 @@
   "wham_docker": "us.gcr.io/broad-dsde-methods/wham:8645aa",
   "igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",
-  "vapor_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/vapor:mw-xz-fixes-2-b1be6a9",
+  "vapor_docker": "us.gcr.io/broad-dsde-methods/eph/vapor:header-hash-2fc8f12",
   "cloud_sdk_docker": "google/cloud-sdk",
   "pangenie_docker": "us.gcr.io/broad-dsde-methods/vjalili/pangenie:vj-127571f",
   "sv-base-virtual-env": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-virtual-env:2022-06-10-v0.23-beta-9c6fbf56",

diff --git a/wdl/TasksBenchmark.wdl b/wdl/TasksBenchmark.wdl
@@ -44,6 +44,7 @@ task ConcatVaPoR {
   command <<<
     set -eu
 
+    zcat ~{shard_bed_files[0]} | head -n1 > header.txt
     # note head -n1 stops reading early and sends SIGPIPE to zcat,
     # so setting pipefail here would result in early termination
 
@@ -54,6 +55,7 @@ task ConcatVaPoR {
     zcat $SPLIT | tail -n+2
       done < ~{write_lines(shard_bed_files)} \
       | sort -Vk1,1 -k2,2n -k3,3n \
+      | cat header.txt - \
       | bgzip -c \
       > ~{output_file}