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 <[email protected]>
IKIM-Essen · Feb 15, 2022 · c5b9f6c · c5b9f6c
1 parent 429e5d9
commit c5b9f6c
Showing 1 changed file with 1 addition and 4 deletions.
diff --git 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: