From 5ad1bd00ce3b397579cc538901c686d50256dc21 Mon Sep 17 00:00:00 2001
From: Thomas Battenfeld <46334240+thomasbtf@users.noreply.github.com>
Date: Wed, 26 Jan 2022 13:29:18 +0100
Subject: [PATCH 1/2] fix: remove removal of .indicators/replacement_notice.txt
 for int

---
 workflow/rules/long_read.smk | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index ba864bb8a..2ff3ccf65 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -32,7 +32,8 @@ rule count_fastq_reads:
         "echo $(( $(cat {input} | wc -l ) / 4)) > {output} 2> {log}"
 
 
-# Intermediate number of threads (4-8) achieve best speedup of a+btrimming.
+# Inte
+ediate number of threads (4-8) achieve best speedup of a+btrimming.
 # For large files 8 threads help accelerate some, small files are processed faster with 4 threads.
 rule porechop_adapter_barcode_trimming:
     input:
@@ -80,10 +81,7 @@ 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:

From 6843d4565c2e24e255f08b474ca23960105cd4fb Mon Sep 17 00:00:00 2001
From: Thomas Battenfeld <thomas.battenfeld@gmail.com>
Date: Wed, 26 Jan 2022 13:44:38 +0100
Subject: [PATCH 2/2] fmt

---
 workflow/rules/long_read.smk | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
index 2ff3ccf65..d4d70afa6 100644
--- a/workflow/rules/long_read.smk
+++ b/workflow/rules/long_read.smk
@@ -32,8 +32,7 @@ rule count_fastq_reads:
         "echo $(( $(cat {input} | wc -l ) / 4)) > {output} 2> {log}"
 
 
-# Inte
-ediate number of threads (4-8) achieve best speedup of a+btrimming.
+# Intermediate number of threads (4-8) achieve best speedup of a+btrimming.
 # For large files 8 threads help accelerate some, small files are processed faster with 4 threads.
 rule porechop_adapter_barcode_trimming:
     input: