Snakemake：通配符限制

Question

我有以下

Snakemake

规则（我只显示了相关部分）：

SAMPLE_IP = ['control_1_hif1a_hyp', 'control_2_hif1a_hyp']
SAMPLE_INPUT = ['control_1_input_hyp', 'control_2_input_hyp']

rule all:
    input:
        expand("bigwig/compare/{sample_ip}_vs_{sample_input}.bw", sample_ip=SAMPLE_IP, sample_input=SAMPLE_INPUT),]
    

rule bigwig_sample_vs_input:
    input:
        ip="mapped/{sample_ip}_dedup.bam",
        inpt="mapped/{sample_input}_dedup.bam",
    output:
        "bigwig/compare/{sample_ip}_vs_{sample_input}.bw",
    params:
        bs=config["general"]["bigwig"]["binSize"],
    threads: config["resources"]["deeptools"]["cpu"]
    resources: 
        runtime=config["resources"]["deeptools"]["time"]
    conda:
        "envs/chipseq.yaml"
    shell:
        "bamCompare -p {threads} -bs {params.bs} -b1 {input.ip} -b2 {input.inpt} "

该规则有效，但

Snakemake

创建了四个具有以下值的

.bw

文件：

sample_input: control_1_input_hyp
sample_ip: control_1_hif1a_hyp

sample_input: control_2_input_hyp
sample_ip: control_1_hif1a_hyp

sample_input: control_1_input_hyp
sample_ip: control_2_hif1a_hyp

sample_input: control_2_input_hyp
sample_ip: control_2_hif1a_hyp

但我只想用：

sample_input: control_1_input_hyp
sample_ip: control_1_hif1a_hyp

sample_input: control_2_input_hyp
sample_ip: control_2_hif1a_hyp

如何告诉

Snakemake

仅组合

SAMPLE_IP

和

SAMPLE_INPUT

中在这些列表中具有相同位置的元素？

Answer 1

使用

zip

中的

expand

选项，规则

input

中的

all

指令将如下所示：

expand("bigwig/compare/{sample_ip}_vs_{sample_input}.bw", zip, sample_ip=SAMPLE_IP, sample_input=SAMPLE_INPUT),]