diff --git a/tasks/utilities/data_export/task_broad_terra_tools.wdl b/tasks/utilities/data_export/task_broad_terra_tools.wdl index 12e79348c..8a54d6bad 100644 --- a/tasks/utilities/data_export/task_broad_terra_tools.wdl +++ b/tasks/utilities/data_export/task_broad_terra_tools.wdl @@ -394,7 +394,8 @@ task export_taxon_tables { volatile: true } command <<< - + set -euo pipefail + # capture taxon and corresponding table names from input taxon_tables taxon_array=($(cut -f1 ~{taxon_tables} | tail +2)) echo "Taxon array: ${taxon_array[*]}" @@ -786,7 +787,7 @@ task export_taxon_tables { "agrvate_version": "~{agrvate_version}", "agrvate_docker": "~{agrvate_docker}", "srst2_vibrio_detailed_tsv": "~{srst2_vibrio_detailed_tsv}", - "srst2_vibrio_version": "~{srst2_vibrio_version}",~ + "srst2_vibrio_version": "~{srst2_vibrio_version}", "srst2_vibrio_docker": "~{srst2_vibrio_docker}", "srst2_vibrio_database": "~{srst2_vibrio_database}", "srst2_vibrio_ctxA": "~{srst2_vibrio_ctxA}",