Snakemake 工作流程独立工作，但作为模块导入时失败

Question

我有两条工作管道。第一个管道从配置文件获取输入，然后创建 .csv 输出文件。第二个管道接收前一个管道的 .csv 输出。当我独立运行这些管道时，它们按预期工作。我试图通过将它们作为模块导入到第三个 Snakefile 中来组合这些管道。然而，snakefile 抛出了一个错误，我无法弄清楚我做错了什么。

我的snakemake版本是8.6

目录结构如下：

• 组合管道
  • 管道1
  • 管道2
  • 组合管道

这是我在其中导入工作管道的 Snakefile 的内容。

from snakemake.utils import min_version
min_version("6.0")


module metadata:
    snakefile:
        "../../metadata/workflow/metadata.smk"
    replace_prefix: '../../metadata'
    config:
        'config/metadata.yaml'

use rule * from metadata as metadata_*

module download:
    snakefile:
        "../../download/workflow/downloads.smk"
    replace_prefix: "../../download"
    config:
        'config/download.yaml'

use rule * from download as download_*

rule all:
    input:
        rules.metadata_all.input,
        rules.download_all.input
    default_target: True

这是我运行时收到的错误

snakemake --cores 1 -n

：

Traceback (most recent call last):
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/cli.py", line 1961, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/api.py", line 328, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/api.py", line 438, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/api.py", line 385, in _workflow
    workflow.include(
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/workflow.py", line 1391, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/home/bayraktar/PycharmProjects/combined_pipelines/run_pipe/workflow/Snakefile", line 16, in <module>
    "../../download/workflow/downloads.smk"
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/workflow.py", line 2130, in decorate
    module.use_rules(
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/modules.py", line 82, in use_rules
    modifier = WorkflowModifier(
               ^^^^^^^^^^^^^^^^^
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/modules.py", line 207, in __init__
    self.path_modifier = PathModifier(replace_prefix, prefix, workflow)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bayraktar/miniforge3/envs/snakemakefull/lib/python3.12/site-packages/snakemake/path_modifier.py", line 32, in __init__
    for prefix, replacement in replace_prefix.items():
                               ^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'items'

Answer 1

错误消息清楚地解释了问题：

replace_prefix

应该是字典，而不是字符串。从逻辑上讲，要替换某些内容，您需要指定要替换的内容以及要替换的内容。所以它应该看起来像这样： replace_prefix: {'../../metadata' : 'absolute_path_to_metadata'}