From 59cfb869cfa4da921c45c63a9ccf7360ea7aee22 Mon Sep 17 00:00:00 2001
From: seehagec01 <seehagec01@mi.fu-berlin.de>
Date: Tue, 26 Apr 2022 11:06:05 +0200
Subject: [PATCH] sambam
---
project/workflow/rules/bowtie2.smk | 2 +-
project/workflow/rules/samtools.smk | 25 ++++++-------------------
2 files changed, 7 insertions(+), 20 deletions(-)
diff --git a/project/workflow/rules/bowtie2.smk b/project/workflow/rules/bowtie2.smk
index 0c1063f..6259d9f 100644
--- a/project/workflow/rules/bowtie2.smk
+++ b/project/workflow/rules/bowtie2.smk
@@ -26,7 +26,7 @@ rule map:
threads:4
conda:
"../envs/yourenv.yaml"
- wrapper:
+ wrapper:
"v1.3.2/bio/bowtie2/align"
diff --git a/project/workflow/rules/samtools.smk b/project/workflow/rules/samtools.smk
index 83a766b..34d0e92 100644
--- a/project/workflow/rules/samtools.smk
+++ b/project/workflow/rules/samtools.smk
@@ -1,30 +1,17 @@
-rule samtool:
+rule fastq:
input:
- "results/sam/{sample}.sam"
+ "results/bam/{sample}.bam"
output:
- "results/unmapped/{sample}_unmapped.sam"
+ "results/unmapped_fastq/{sample}_1_unmapped.fastq",
+ "results/unmapped_fastq/{sample}_2_unmapped.fastq"
log:
- "workflow/report/samtools/{sample}.log"
- threads:4
- conda:
- "../envs/yourenv.yaml"
- shell:
- "samtools view --threads {threads} -f4 {input} > {output}"
-
-rule converts:
- input:
- "results/unmapped/{sample}_unmapped.sam"
- output:
- "results/unmapped_converts/{sample}_1_unmapped.fastq",
- "results/unmapped_converts/{sample}_2_unmapped.fastq"
- log:
- "workflow/report/converts/{sample}.log"
+ "workflow/report/fastq/{sample}.log"
threads:4
conda:
"../envs/yourenv.yaml"
shell:
"""
- samtools view -S -b --threads={threads} {input} > {wildcards.sample}_unmapped.bam 2> {log}
+ samtools view --threads={threads} -b -f4 {input} > {wildcards.sample}_unmapped.bam 2> {log} #extract unmapped reads
samtools sort -n {wildcards.sample}_unmapped.bam -o {wildcards.sample}_sorted.bam 2>> {log}
bedtools bamtofastq -i {wildcards.sample}_sorted.bam -fq {output[0]} -fq2 {output[1]} 2>> {log}
"""
--
GitLab