蛇形是否支持无文件输入?

如何解决蛇形是否支持无文件输入?

运行以下规则时得到 MissingInputException

configfile: "Configs.yaml"

rule download_data_from_ZFIN:
    input:
        anatomy_item = config["ZFIN_url"]["anatomy_item"],xpat_stage_anatomy = config["ZFIN_url"]["xpat_stage_anatomy"],xpat_fish = config["ZFIN_url"]["xpat_fish"],anatomy_synonyms = config["ZFIN_url"]["anatomy_synonyms"]
    output:
        anatomy_item = os.path.join(os.getcwd(),config["download_data_from_ZFIN"]["dir"],"anatomy_item.tsv"),xpat_stage_anatomy = os.path.join(os.getcwd(),"xpat_stage_anatomy.tsv"),xpat_fish = os.path.join(os.getcwd(),"xpat_fish.tsv"),anatomy_synonyms = os.path.join(os.getcwd(),"anatomy_synonyms.tsv")
    shell:
        "wget -O {output.anatomy_item} {input.anatomy_item};" \
        "wget -O {output.anatomy_synonyms} {input.anatomy_synonyms};" \
        "wget -O {output.xpat_stage_anatomy} {input.xpat_stage_anatomy};" \
        "wget -O {output.xpat_fish} {input.xpat_fish};"

这是我的 configs.yaml 文件的内容:

ZFIN_url:
  # Zebrafish Anatomy Term
  anatomy_item: "https://zfin.org/downloads/file/anatomy_item.txt"
  # Zebrafish Gene Expression by Stage and Anatomy Term
  xpat_stage_anatomy: "https://zfin.org/downloads/file/xpat_stage_anatomy.txt"
  # ZFIN Genes with Expression Assay Records
  xpat_fish: "https://zfin.org/downloads/file/xpat_fish.txt"
  # Zebrafish Anatomy Term Synonyms
  anatomy_synonyms: "https://zfin.org/downloads/file/anatomy_synonyms.txt"

download_data_from_ZFIN:
  dir: ZFIN_data

错误信息是:

Building DAG of jobs...
MissingInputException in line 10 of /home/zhangdong/works/NGS/coevolution/snakemake/coevolution.rule:
Missing input files for rule download_data_from_ZFIN:
https://zfin.org/downloads/file/anatomy_item.txt

我想确定此异常是否是由 input 规则的无文件输入引起的?

解决方法

请注意,您也可以使用 remote files 作为输入,这样您就可以完全避免规则 download_data_from_ZFIN。例如:

from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider

HTTP = HTTPRemoteProvider()

rule all:
    input:
        'output.txt',rule one:
    input:
        # Some file from the web
        x= HTTP.remote('https://plasmodb.org/common/downloads/release-49/PbergheiANKA/txt/PlasmoDB-49_PbergheiANKA_CodonUsage.txt',keep_local=True)
    output:
        'output.txt',shell:
        r"""
        # Do something with the remote file
        head {input.x} > {output}
        """

远程文件将被下载并存储在本地plasmodb.org/common/.../PlasmoDB-49_PbergheiANKA_CodonUsage.txt

,

非常感谢@dariober,我尝试了以下代码并且成功了,

import os
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
configfile: "Configs.yaml"

HTTP = HTTPRemoteProvider()

rule all:
    input:
        expand(os.path.join(os.getcwd(),config["download_data_from_ZFIN"]["dir"],"{item}.tsv"),item=list(config["ZFIN_url"].keys()))

rule download_data_from_ZFIN:
    input:
        lambda wildcards: HTTP.remote(config["ZFIN_url"][wildcards.item],keep_local=True)
    output:
        os.path.join(os.getcwd(),"{item}.tsv")
    threads:
        1
    shell:
        "mv {input} > {output}"

这样的代码更像蛇形,但我还有两个问题:

  1. 有没有办法指定下载的输出文件名?现在我使用 mv 命令来实现这一点。
  2. remote files 函数是否支持并行工作?我把上面的代码和--cores 6一起试了,但是还是一个一个的下载文件。

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