From bea2b3f833ba0cb3f9fa26053c01a448d1400a28 Mon Sep 17 00:00:00 2001
From: cimendes <iines.mendes@gmail.com>
Date: Fri, 30 Sep 2022 11:55:43 +0100
Subject: [PATCH] Update assembly.nf

---
 modules/assembly/assembly.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/assembly/assembly.nf b/modules/assembly/assembly.nf
index 1f159ef..6a65390 100644
--- a/modules/assembly/assembly.nf
+++ b/modules/assembly/assembly.nf
@@ -373,11 +373,13 @@ process STRAINXPRESS {
     echo '' > .${sample_id}_strainxpress_version
     {
         python3 /NGStools/StrainXpress/scripts/strainxpress.py -fq $fasta_reads_single -t $task.cpus
-
-        mv all.contigs_*.fasta ${sample_id}_strainxpress.fasta
         echo pass > .status
     } || {
         echo fail > .status
+    }
+    {
+        mv stageb/final_contigs.fasta ${sample_id}_strainxpress.fasta
+    } || {
         :> ${sample_id}_strainxpress.fasta
     }
     """