NameError：运行snakemake时未定义名称“snakemake”

Question

我有一个示例脚本定义为：

#!/usr/bin/env python

def test(path):
    print(path)

test(snakemake.input[0])

config.yml 如下：

executor: slurm
jobs: 100
samples: "config/samples.csv"

还有像这样的 Snakefile：

import os
import glob
import pandas as pd

configfile: "config/config.yml"

rule get_samples:
    resources:
        mem_mb = 512
    threads: 1
    input: config["samples"]
    output: "out/sampleFASTQs.csv"
    shell: "scripts/getFASTQs.py"

当我跑步时

snakemake --核心 1

我收到以下错误：

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job            count    min threads    max threads
-----------  -------  -------------  -------------
get_samples        1              1              1
total              1              1              1

Select jobs to execute...

[Wed May 15 05:36:05 2024]
rule get_samples:
    input: config/samples.csv
    output: out/sampleFASTQs.csv
    jobid: 0
    reason: Missing output files: out/sampleFASTQs.csv
    resources: tmpdir=/tmp, mem_mb=512, mem_mib=489

Traceback (most recent call last):
  File "[redacted]/tools/snakemake/scrnaseq/workflow/scripts/getFASTQs.py", line 6, in <module>
    test(snakemake.input[0])
NameError: name 'snakemake' is not defined
[Wed May 15 05:36:05 2024]
Error in rule get_samples:
    jobid: 0
    input: config/samples.csv
    output: out/sampleFASTQs.csv
    shell:
        scripts/getFASTQs.py
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-05-15T053604.329295.snakemake.log

我几乎在任何地方都找不到这个错误，也不明白为什么 python 环境中没有自动定义 Snakemake。

Answer 1

如果您使用

run

指令（而不是

shell

），那么代码块将继承 Snakefile 内的所有内容。

如果使用

script

指令，那么脚本将继承

snakemake

对象。

更多信息可以在docs中找到。