From c5b9f6c02c6e65646d0bc748cef5962b56322b3e Mon Sep 17 00:00:00 2001
From: Thomas Battenfeld <46334240+thomasbtf@users.noreply.github.com>
Date: Tue, 15 Feb 2022 15:44:02 +0100
Subject: [PATCH] fix: remove removal of .indicators/replacement_notice.txt for
 int (#457)

* fix: remove removal of .indicators/replacement_notice.txt for int

* fmt

Co-authored-by: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
---
 workflow/rules/long_read.smk | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index ba864bb8a..d4d70afa6 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -80,10 +80,7 @@ rule porechop_primer_trimming:
         "logs/{date}/trimmed/porechop/primer_clipped/{sample}.log",
     threads: 2
     shell:
-        """
-        (porechop -i {input.fastq_in} -o {output} --no_split --end_size 35 --extra_end_trim 0 -t {threads} -v 1) 2> {log}
-        rm results/.indicators/replacement_notice.txt
-        """
+        "(porechop -i {input.fastq_in} -o {output} --no_split --end_size 35 --extra_end_trim 0 -t {threads} -v 1) 2> {log}"
 
 
 rule nanofilt: