From b265ed7fe58200c4b9551d09a2b35ac9cca65f91 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 19 Nov 2020 15:28:19 +0100
Subject: [PATCH] mv output dir to params
---
tools/strainphlan/sample2markers/Snakefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/tools/strainphlan/sample2markers/Snakefile b/tools/strainphlan/sample2markers/Snakefile
index c9ee84c..a577299 100644
--- a/tools/strainphlan/sample2markers/Snakefile
+++ b/tools/strainphlan/sample2markers/Snakefile
@@ -8,11 +8,11 @@ rule sample2markers:
input:
__sample2markers_input
output:
- dir = __sample2markers_output_dir,
- file = __sample2markers_output
+ __sample2markers_output
params:
exec_command = __sample2markers_exec_command,
modules = __sample2markers_modules,
+ output_dir = __sample2markers_output_dir,
options = __sample2markers_options
threads:
__sample2markers_threads
@@ -20,5 +20,5 @@ rule sample2markers:
command = []
if params.modules:
command.append("module load {params.modules}")
- command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {output.dir}")
+ command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {params.output_dir}")
shell(" && ".join(command))
--
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