From ed0d5890cf9cca882eb61554f72db28e1d42ee60 Mon Sep 17 00:00:00 2001
From: Sage Wright <40403716+sage-wright@users.noreply.github.com>
Date: Tue, 26 Apr 2022 13:52:43 -0400
Subject: [PATCH] added variable `pangolin_arguments` (#139)

---
 tasks/task_taxonID.wdl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tasks/task_taxonID.wdl b/tasks/task_taxonID.wdl
index 8f9e1b8b..0ec524e2 100644
--- a/tasks/task_taxonID.wdl
+++ b/tasks/task_taxonID.wdl
@@ -129,6 +129,7 @@ task pangolin4 {
     Float max_ambig = 0.5
     String docker = "quay.io/staphb/pangolin:4.0.4-pdata-1.2.133"
     String? analysis_mode
+    String? pangolin_arguments
   }
   command <<<
     set -e
@@ -143,7 +144,8 @@ task pangolin4 {
        ~{'--min-length ' + min_length} \
        ~{'--max-ambig ' + max_ambig} \
        --outfile "~{samplename}.pangolin_report.csv" \
-       --verbose
+       --verbose \
+       ~{pangolin_arguments}
 
     python3 <<CODE
     import csv