diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json index 423aeb8a0..fd4e2241c 100644 --- 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 index 021ccd83d..70296c89f 100644 --- 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}