From ac67e684281abf2662c8dd7ab57f4726934321dd Mon Sep 17 00:00:00 2001
From: Mike Lloyd <mike.lloyd@jax.org>
Date: Thu, 18 Jul 2024 15:27:38 -0400
Subject: [PATCH] escape fix

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

diff --git a/modules/xengsort/xengsort_classify.nf b/modules/xengsort/xengsort_classify.nf
index 99eaa51..1c88f63 100644
--- a/modules/xengsort/xengsort_classify.nf
+++ b/modules/xengsort/xengsort_classify.nf
@@ -42,8 +42,8 @@ process XENGSORT_CLASSIFY {
         --chunksize 32.0 \
         --compression none &> ${sampleID}_xengsort_log.txt
 
-        cat fastq-host.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" > ${sampleID}_fastq-host_sorted.1.fq
-        cat fastq-graft.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" > ${sampleID}_fastq-graft_sorted.1.fq
+        cat fastq-host.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-host_sorted.1.fq
+        cat fastq-graft.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-graft_sorted.1.fq
 
         """