我正在尝试使用snakemake运行hisat2映射。 基本上,我使用的是config.yaml文件,如下所示:
reads:
set1: /path/to/set1/samplelist.tab
hisat2:
database: genome
genome: genome.fa
nodes: 2
memory: 8G
arguments: --dta
executables:
hisat2: /Tools/hisat2-2.1.0/hisat2
samtools: /Tools/samtools-1.3/samtools
然后创建snakefile:
configfile: "config.yaml"
workdir: "/path/to/working_dir/"
# Hisat2
rule hisat2:
input:
reads = lambda wildcards: config["reads"][wildcards.sample]
output:
bam = "{sample}/{sample}.bam"
params:
idx=config["hisat2"]["database"],executable = config["executables"]["hisat2"],nodes = config["hisat2"]["nodes"],memory = config["hisat2"]["memory"],executable2 = config["executables"]["samtools"]
run:
shell("{params.executable} --dta -p {params.nodes} -x {params.idx} {input.reads} |"
"{params.executable2} view -Sbh -o {output.bam} -")
# all
rule all:
input:
lambda wildcards: [sample + "/" + sample + ".bam"
for sample in config["reads"].keys()]
我的samplelist.tab是这样的:
id reads1 reads2
set1a set1a_R1.fastq.gz set1a_R2.fastq.gz
set1b set1b_R1.fastq.gz set1b_R2.fastq.gz
任何提示如何使它起作用的?我为一个凌乱的脚本提出了要求,只是开始使用snakemake。