From e60c44c96917cc1cae0ce933e4895c68f9208900 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 19 Nov 2020 15:04:56 +0100
Subject: [PATCH] update paired metaphlan with new outputs
---
tools/metaphlan3/metaphlan/paired/Snakefile | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/tools/metaphlan3/metaphlan/paired/Snakefile b/tools/metaphlan3/metaphlan/paired/Snakefile
index 3e41c2f..5517590 100644
--- a/tools/metaphlan3/metaphlan/paired/Snakefile
+++ b/tools/metaphlan3/metaphlan/paired/Snakefile
@@ -18,13 +18,13 @@ rule metaphlan3_paired:
r1 = __metaphlan3_input_r1,
r2 = __metaphlan3_input_r2
output:
- __metaphlan3_output
+ profile = __metaphlan3_output,
+ bowtie2out = __metaphlan3_output_bowtie2out,
+ sams = __metaphlan3_output_sams
params:
exec_command = __metaphlan3_exec_command,
modules = __metaphlan3_modules,
input_type = __metaphlan3_input_type,
- bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
- sams = "{output_dir}/{sample}.sam.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
options = __metaphlan3_options
threads:
__metaphlan3_threads
@@ -32,5 +32,5 @@ rule metaphlan3_paired:
command = []
if params.modules:
command.append("module load {params.modules}")
- command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {params.sams} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
+ command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} -s {output.sams} --bowtie2out {output.bowtie2out} {params.options} {input.r1},{input.r2} {output.profile}")
shell(" && ".join(command))
--
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