Snakemake 复制一个文件到多个文件

Question

我有几个文件夹

folder_1234
folder_4321

我想从一个文件夹（已经存在）复制一个文件myfile.sh到所有文件夹，然后使用sed:

更改文件内的数字

SAMPLE=["1234","4321"]
rule all:
    input:
        expand("workdir/folder_{sample}/myfile.sh", sample=SAMPLES)
rule copy:
    input:
        copy_from="/path/to/folder_1234/myfile.sh"
    output:
        copy_to="workdir/folder_{sample}/myfile.sh"
    shell:
        """
        cp {input.copy_from} {output.copy_to}
        sed "s/folder_1234/folder_{sample}/g" folder_{sample}/myfile.sh
        """

这给了我一个错误：

NameError: The name 'sample' is unknown in this context. Did you mean 'wildcards.sample'?

Answer 1

在shell命令中，这里的通配符语法是{wildcards.sample}而不是{sample}。有关通配符用法的文档，see here.

Snakemake 复制一个文件到多个文件

Snakemake copy one file to multiple files

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