From 5bcb25b36805faaf13e9bdd3e825e298ec8ad759 Mon Sep 17 00:00:00 2001
From: Sage Wright <sage.wright@theiagen.com>
Date: Mon, 21 Oct 2024 17:33:48 +0000
Subject: [PATCH] remove exit 1 because it's causing task to fail

---
 tasks/assembly/task_metaspades.wdl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tasks/assembly/task_metaspades.wdl b/tasks/assembly/task_metaspades.wdl
index 45b71532d..4982e3521 100644
--- a/tasks/assembly/task_metaspades.wdl
+++ b/tasks/assembly/task_metaspades.wdl
@@ -32,12 +32,10 @@ task metaspades_pe {
       if [ ! -s ~{samplename}_contigs.fasta ]; then
         tee "Metaspades produced an empty assembly for ~{samplename}" > WARNING
         rm -f ~{samplename}_contigs.fasta
-        exit 1
       fi
     
     else
       tee "Metaspades failed to assemble for ~{samplename}" > WARNING
-      exit 1
     fi
 
   >>>