Skip to content
Snippets Groups Projects
Commit d59c4f5d authored by Dominik Burri's avatar Dominik Burri
Browse files

correct python tabs

parent 739bd4cf
No related branches found
No related tags found
1 merge request!39Alfa qc
Pipeline #10061 passed
Stage: test
Hide whitespace changes
Inline Side-by-side
Showing
with 8 additions and 8 deletions
snakemake/Snakefile
+ 8
− 8
View file @ d59c4f5d
...@@ -156,16 +156,16 @@ rule generate_alfa_index: ...@@ -156,16 +156,16 @@ rule generate_alfa_index:
-p {threads} \ -p {threads} \
-o {params.out_dir} &> {log}" -o {params.out_dir} &> {log}"
rule star_rpm: rule star_rpm_stranded:
''' Create bedgraph coverage with STARs RPM normalisation ''' ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
input: input:
"/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam" "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
output: output:
"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg", "/scicore/home/zavolan/burri0000/rnaseqpipeline/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.str2.out.bg"
params: params:
out_dir = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/", out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/",
filenameprefix = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_" filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_"
singularity: singularity:
"docker://zavolab/star:2.6.0a" "docker://zavolab/star:2.6.0a"
threads: 4 threads: 4
...@@ -187,8 +187,8 @@ rule star_rpm: ...@@ -187,8 +187,8 @@ rule star_rpm:
rule run_alfa_bg_stranded: rule run_alfa_bg_stranded:
''' Run ALFA from stranded bedgraph files ''' ''' Run ALFA from stranded bedgraph files '''
input: input:
"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg", str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg" str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
output: output:
directory("output/") directory("output/")
params: params:
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment