snakemake 基于 python3。
snakemake基本命令
每一个部分包含输入输出和命令
蓝色方框是4个空格
举一个最简单的例子
samples = ["A", "B"]
rule all:
input: expand("results/{sample}.txt", sample=samples)
rule align:
input: "raw/{sample}.fq"
output: "bam/{sample}.bam"
shell: "bwa mem ref.fa {input} | samtools view -b > {output}"
rule count:
input: "bam/{sample}.bam"
output: "results/{sample}.txt"
shell: "featureCounts -a ref.gtf -o {output} {input}"
检查写的pipeline有没有问题
snakemake -s XXXX.py -n -p
生成拓扑图
snakemake -s XXXX.py --dog | dot -Tpdf > test_dog.pdf
运行
snakemake -s XXXX.py -p -j 2 &
运行snakemake
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