snakemake

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