Question

我开始为我的生物信息学项目编写管道，并且我使用Snakemake作为工作流程。我制作了官方网站的所有教程和一些文档。

我想运行一个shell命令，就像这样： fastp -i input-1 -I input-2 -o output-1 -O output-2

我在Snakefile中的代码：

SAMPLES = ['1', '2', '3', '4']
rule fastp:
    input:
        reads1=expand("sample{sample}.R1.fq.gz", sample=SAMPLES),
        reads2=expand("sample{sample}.R2.fq.gz", sample=SAMPLES)
    output:
        reads1out=expand("sample{sample}.R1.fq.gz.out", sample=SAMPLES),
        reads2out=expand("sample{sample}.R2.fq.gz.out", sample=SAMPLES)
    shell:
        "fastp -i {input.reads1} -I {input.reads2} -o {output.reads1out} -O {output.reads2out}"

但程序运行这一行代码：fastp -i sample1.R1.fq.gz sample2.R1.fq.gz sample3.R1.fq.gz sample4.R1.fq.gz -I sample1.R2.fq.gz sample2.R2.fq.gz sample3.R2.fq.gz sample4.R2.fq.gz -o sample1.R1.fq.gz.out sample2.R1.fq.gz.out sample3.R1.fq.gz.out sample4.R1.fq.gz.out -O sample1.R2.fq.gz.out sample2.R2.fq.gz.out sample3.R2.fq.gz.out sample4.R2.fq.gz.out

如何编写程序为每个样本执行不同的shell命令？我在for i in SAMPLES:之后尝试rule fastp:，但没有工作，我不知道我现在可以尝试什么。很抱歉，如果这个主题在某种程度上太基础，但我是Python中的菜鸟。

谢谢。

Answer 1

您需要define target使用rule all输出文件。

SAMPLES = ['1', '2', '3', '4']
rule all:
    input:
        expand("sample{sample}.R{read_no}.fq.gz.out", sample=SAMPLES, read_no=['1', '2'])

rule fastp:
    input:
        reads1="sample{sample}.R1.fq.gz",
        reads2="sample{sample}.R2.fq.gz"
    output:
        reads1out="sample{sample}.R1.fq.gz.out",
        reads2out="sample{sample}.R2.fq.gz.out"
    shell:
        "fastp -i {input.reads1} -I {input.reads2} -o {output.reads1out} -O {output.reads2out}"

Answer 2

这是命令snakemake -np的输出，带有rule all: ，正如JeeYem所写：

λ fastp/testdata master ✗ snakemake -np rule fastp: input: sample1.R1.fq.gz, sample2.R1.fq.gz, sample3.R1.fq.gz, sample4.R1.fq.gz, sample1.R2.fq.gz, sample2.R2.fq.gz, sample3.R2.fq.gz, sample4.R2.fq.gz output: sample1.R1.fq.gz.out, sample2.R1.fq.gz.out, sample3.R1.fq.gz.out, sample4.R1.fq.gz.out, sample1.R2.fq.gz.out, sample2.R2.fq.gz.out, sample3.R2.fq.gz.out, sample4.R2.fq.gz.out jobid: 1 fastp -i sample1.R1.fq.gz sample2.R1.fq.gz sample3.R1.fq.gz sample4.R1.fq.gz -I sample1.R2.fq.gz sample2.R2.fq.gz sample3.R2.fq.gz sample4.R2.fq.gz -o sample1.R1.fq.gz.out sample2.R1.fq.gz.out sample3.R1.fq.gz.out sample4.R1.fq.gz.out -O sample1.R2.fq.gz.out sample2.R2.fq.gz.out sample3.R2.fq.gz.out sample4.R2.fq.gz.out localrule all: input: sample1.R1.fq.gz.out, sample1.R2.fq.gz.out, sample2.R1.fq.gz.out, sample2.R2.fq.gz.out, sample3.R1.fq.gz.out, sample3.R2.fq.gz.out, sample4.R1.fq.gz.out, sample4.R2.fq.gz.out jobid: 0 Job counts: count jobs 1 all 1 fastp 2

Snakemake使用多输入

2 个答案: