From 0700387713d7dfdbd858d6d6431ca6bb1b69ec15 Mon Sep 17 00:00:00 2001
From: Rachel LEGENDRE <rachel.legendre@pasteur.fr>
Date: Mon, 13 Mar 2023 17:01:27 +0100
Subject: [PATCH] Update cutadapt.rules
---
workflow/rules/cutadapt.rules | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index 9e6364b..4d5ee2c 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -49,16 +49,18 @@ rule cutadapt:
tmp="{output}"
outfiles=($tmp)
+ mode="{params.mode}"
+
# add mode and adapter sequences
- cmd+=" cutadapt -j {threads} -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options} "
+ cmd+=" cutadapt -${{mode}} {params.adapters} -m {params.min} -q {params.qual} {params.options} -j {threads} "
# paired end or single end
if [[ ${{#infiles[@]}} -eq 2 ]];
then
- cmd+=" -o ${{outfiles[0]}} -p ${{outfiles[1]}} ${{infiles[0]}} ${{infiles[1]}} "
+ cmd+=" -${{mode^^}} {params.adapters} -o ${{outfiles[0]}} -p ${{outfiles[1]}} ${{infiles[0]}} ${{infiles[1]}} "
else
cmd+=" -o ${{outfiles[0]}} ${{infiles[0]}}"
fi
#run command
- eval "${{cmd}} > {log.out}"
+ eval "${{cmd}} > {log}"
"""
--
GitLab