Snakemake-下载数据的规则 [英] Snakemake - rule that downloads data

问题描述

我在实施管道时遇到了一些麻烦，在该管道中，第一步是从某些服务器下载数据.据我了解，所有规则都必须具有作为文件的输入.但是，在我的情况下，输入"是提供给脚本的ID字符串，该脚本访问服务器并下载数据.
我知道了snakemake中的远程文件选项，但是服务器我从( ENA )下载的文件不在该列表中.此外，我正在使用一个调用aspera的脚本来提高下载速度.
关于如何在snakemake中实现这种方案的任何想法?

I am having some trouble implementing a pipeline in which the first step is downloading the data from some server. As far as I understand, all rules must have inputs which are files. However, in my case the "input" is an ID string given to a script which accesses the server and downloads the data.
I am aware of the remote files option in snakemake, but the server I am downloading from (ENA) is not on that list. Moreover, I am using a script which calls aspera in order to improve download speed.
Any ideas of how such a scenario can be implemented in snakemake?

推荐答案

规则实际上不需要输入字段，因此可能是这样:

Rules actually do not need an input field, so sth like this is possible:

rule download:
    output:
        "downloads/{sample}.fa"
    shell:
        "ascp ftp:/url_here+{wildcards.sample}"

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