From 4af9f0b1923c12d1935b6b6ef57b7418a0d512ba Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 24 Jan 2020 14:51:52 +0100
Subject: [PATCH] ALFA (un)stranded works for chr21.bam #18
---
snakemake/Snakefile | 64 +++++++++++++++++++++++++++------------------
1 file changed, 38 insertions(+), 26 deletions(-)
diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index ddb3e63..79bb791 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -149,27 +149,31 @@ rule generate_alfa_index:
singularity:
"docker://zavolab/alfa:1.1.1"
log:
- "generate_alfa_index.log"
+ "logs/generate_alfa_index.log"
shell:
"alfa -a {input.gtf} \
-g {params.genome_index} \
-p {threads} \
-o {params.out_dir} &> {log}"
+# TODO: test with chr21.bam
+# add singularity-args to this chr21.bam path
rule star_rpm_stranded:
''' Create stranded bedgraph coverage with STARs RPM normalisation '''
input:
- "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
+ bam = "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
output:
- "/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"
+ str1 = ("/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.Unique.str1.out.bg",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str1.out.bg"),
+ str2 = ("/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg")
params:
- out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/",
- filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_"
+ out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/",
+ filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_"
singularity:
"docker://zavolab/star:2.6.0a"
threads: 4
- log: "logs/star_rpm.log"
+ log: "logs/star_rpm_stranded.log"
shell:
"""
(mkdir -p {params.out_dir}; \
@@ -177,31 +181,38 @@ rule star_rpm_stranded:
STAR \
--runMode inputAlignmentsFromBAM \
--runThreadN {threads} \
- --inputBAMfile {input} \
+ --inputBAMfile {input.bam} \
--outWigType "bedGraph" \
--outWigStrand "Stranded" \
--outWigNorm "RPM" \
--outFileNamePrefix {params.filenameprefix}) &> {log}
"""
+# TODO: test with chr21.bam
rule run_alfa_bg_stranded:
''' Run ALFA from stranded bedgraph files '''
input:
- 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"
+ str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str1.out.bg",
+ str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg"
output:
- directory("output/")
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/ALFA_plots.Biotypes.pdf",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/ALFA_plots.Categories.pdf"
params:
- genome_index = "sorted_genes"
+ out_dir = "alfa_stranded",
+ in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
+ in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
+ genome_index = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_index/sorted_genes",
+ name_str1 = "test_chr21_str1",
+ name_str2 = "test_chr21_str2"
+ singularity:
+ "docker://zavolab/alfa:1.1.1"
+ log: "../logs/alfa_bg_stranded.log"
shell:
"""
+ cd {params.out_dir}; \
alfa -g {params.genome_index} \
- -bedgraph {input} \
- -s forward; \
- alfa -g {params.genome_index} \
- -bedgraph {input} \
- -s reverse \
- -o {output}
+ --bedgraph {params.in_file_str1} {params.name_str1} {params.in_file_str2} {params.name_str2} \
+ &> {log}
"""
rule star_rpm_unstranded:
@@ -209,14 +220,15 @@ rule star_rpm_unstranded:
input:
bam = "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
output:
- "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.Unique.str1.out.bg",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.UniqueMultiple.str1.out.bg"
params:
- out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/",
- filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_"
+ out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/",
+ filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_"
singularity:
"docker://zavolab/star:2.6.0a"
threads: 4
- log: "logs/star_rpm.log"
+ log: "logs/star_rpm_unstranded.log"
shell:
"""
(mkdir -p {params.out_dir}; \
@@ -234,12 +246,12 @@ rule star_rpm_unstranded:
rule run_alfa_bg_unstranded:
''' Run ALFA from unstranded bedgraph files '''
input:
- "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.UniqueMultiple.str1.out.bg"
output:
- "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Biotypes.pdf",
- "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Categories.pdf"
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/ALFA_plots.Biotypes.pdf",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/ALFA_plots.Categories.pdf"
params:
- out_dir = "star_rpm",
+ out_dir = "alfa_unstranded",
in_file = "STAR_Signal.UniqueMultiple.str1.out.bg",
genome_index = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_index/sorted_genes",
name = "test_chr21"
--
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