From d19f7b4638561dd223fd24470736c3a8f8755a9a Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Mon, 19 Nov 2018 11:59:43 +0100
Subject: [PATCH] Addition of rule that removes multimappers in the process
data pipeline
---
snakemake/process_data/Snakefile | 19 +++++++++++++++++--
snakemake/process_data/config.yaml | 4 +++-
2 files changed, 20 insertions(+), 3 deletions(-)
diff --git a/snakemake/process_data/Snakefile b/snakemake/process_data/Snakefile
index df87399..3136843 100644
--- a/snakemake/process_data/Snakefile
+++ b/snakemake/process_data/Snakefile
@@ -1,7 +1,7 @@
configfile: "config.yaml"
#from snakemake.utils import listfiles
-localrules: create_output_and_log_directories, finish
+localrules: create_output_and_log_directories, remove_multimappers, finish
#################################################################################
### Finish rule
@@ -9,7 +9,7 @@ localrules: create_output_and_log_directories, finish
rule finish:
input:
- sam = expand(os.path.join(config["output_dir"], "{sample}/transcripts.mapped.sam"), sample=config["sample"])
+ sam = expand(os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.sam"), sample=config["sample"])
#################################################################################
### Create output and log directories
@@ -210,3 +210,18 @@ rule map_to_transcripts:
--threads {threads} \
-o {output.sam} \
-u {output.reads} ) &> {log}"
+
+################################################################################
+### Remove multimappers
+################################################################################
+
+rule remove_multimappers:
+ input:
+ sam = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.sam")
+ output:
+ sam = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.sam")
+ log:
+ os.path.join(config["local_log"], "remove_multimappers_{sample}.log")
+ threads: 1
+ shell:
+ "(grep -P \"^@|\tNH:i:1\t\" {input.sam} > {output.sam}) &> {log}"
diff --git a/snakemake/process_data/config.yaml b/snakemake/process_data/config.yaml
index 6a99137..fb70bb0 100644
--- a/snakemake/process_data/config.yaml
+++ b/snakemake/process_data/config.yaml
@@ -18,7 +18,9 @@
##############################################################################
input_dir: "samples"
input_reads_pattern: ".fastq.gz"
- sample: ["example", "example2"]
+ sample: ["example", "example2", "SRR1536304", "SRR1536305"]
example: {adapter: GATCGGAAGAGCACA, minimum_quality: 20, quality_type: 33}
example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64}
+ SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
+ SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
...
--
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