From d59c4f5de7c72a9b4ce0ed50f7ff7fc239ca1a2f Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 24 Jan 2020 12:13:45 +0100
Subject: [PATCH] correct python tabs
---
snakemake/Snakefile | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index e9eee45..ddb3e63 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -156,16 +156,16 @@ rule generate_alfa_index:
-p {threads} \
-o {params.out_dir} &> {log}"
-rule star_rpm:
- ''' Create bedgraph coverage with STARs RPM normalisation '''
+rule star_rpm_stranded:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
input:
"/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
output:
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
params:
- out_dir = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/",
- filenameprefix = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_"
+ out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/",
+ filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_"
singularity:
"docker://zavolab/star:2.6.0a"
threads: 4
@@ -187,8 +187,8 @@ rule star_rpm:
rule run_alfa_bg_stranded:
''' Run ALFA from stranded bedgraph files '''
input:
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+ str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+ str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
output:
directory("output/")
params:
--
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