fix output type of vadr_alerts

broadinstitute · Jan 23, 2025 · 76b9d99 · 76b9d99
1 parent b129529
commit 76b9d99
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -1580,7 +1580,7 @@ task vadr {
     File                 feature_tbl = "~{out_base}.vadr.tbl"
     Int                  num_alerts  = read_int("NUM_ALERTS")
     File                 alerts_list = "~{out_base}/~{out_base}.vadr.alt.list"
-    Array[Array[String]] alerts      = read_tsv("~{out_base}.vadr.alerts.tsv")
+    Array[String]        alerts      = read_lines("~{out_base}.vadr.alerts.tsv")
     File                 outputs_tgz = "~{out_base}.vadr.tar.gz"
     Boolean              pass        = num_alerts==0
     String               vadr_docker = docker

diff --git a/pipes/WDL/workflows/genbank_single.wdl b/pipes/WDL/workflows/genbank_single.wdl
@@ -130,8 +130,8 @@ workflow genbank_single {
         File          genbank_source_table   = biosample_to_genbank.genbank_source_modifier_table
         File          annotation_tbl         = feature_tbl
 
-        Boolean?             vadr_pass       = vadr.pass
-        Array[Array[String]] vadr_alerts     = select_first([vadr.alerts, [[]]])
+        Boolean?      vadr_pass              = vadr.pass
+        Array[String] vadr_alerts            = select_first([vadr.alerts, []])
 
         File?         genbank_submission_sqn = table2asn.genbank_submission_sqn
         File?         genbank_preview_file   = table2asn.genbank_preview_file