Snakemake-尝试使用global_wildcards时出现问题（TypeError：预期的str，得到了列表）

Question

我是使用Snakemake的新手，也不是Python方面的专家，所以答案可能很明显。在我的测试中，工作流中的所有内容都可以正常运行，直到我尝试使用glob_wildcards，以将我的所有fastq.gz文件从一个目录（FASTQDIR）转换为fastqc文件。

SAMPLES列表中的样本名称是可以的，但是我有一个错误，说应该使用字符串而不是列表（我认为这是我的SAMPLES列表），而且我真的不知道where会在其中起作用我的Snakefile来纠正它。我知道它肯定与我对glob_wildcards的使用有关，但我不知道问题出在哪里。您是否知道我该如何解决？

这是我的Snakefile代码：

FASTQDIR = "/fastq/files/directory/"
WDIR = "/my/working/directory/"
SAMPLES, = glob_wildcards(FASTQDIR + "{sample}.fastq.gz")

rule all:
    input:
        expand(WDIR + "Fastqc/{sample}_fastqc.html", sample=SAMPLES),
        expand(WDIR + "Fastqc/{sample}_fastqc.zip", sample=SAMPLES)

#Generates fastqc file for the sample fastq.gz file in the Fastqc directory
rule fastqc_generate_qc:
    input:
        expand(FASTQDIR + "{sample}.fastq.gz", sample=SAMPLES)
    output:
        expand(WDIR + "Fastqc/{sample}_fastqc.html", sample=SAMPLES),
        expand(WDIR + "Fastqc/{sample}_fastqc.zip", sample=SAMPLES)
    shell:
        "fastqc --outdir Fastqc/ {input}"

这里是整个Traceback：

Traceback (most recent call last):
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/__init__.py", line 420, in snakemake
    force_use_threads=use_threads)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/workflow.py", line 480, in execute
    success = scheduler.schedule()
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/scheduler.py", line 215, in schedule
    self.run(job)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/scheduler.py", line 229, in run
    error_callback=self._error)
  File "/home/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/executors.py", line 59, in run
    self._run(job)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/executors.py", line 120, in _run
    super()._run(job)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/executors.py", line 66, in _run
    self.printjob(job)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/executors.py", line 85, in printjob
    msg=job.message,
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/jobs.py", line 175, in message
    self.rule.message else None)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/jobs.py", line 542, in format_wildcards
    return format(string, **_variables)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/site-packages/snakemake/utils.py", line 259, in format
    return fmt.format(_pattern, *args, **variables)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/string.py", line 187, in format
    return self.vformat(format_string, args, kwargs)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/string.py", line 191, in vformat
    result, _ = self._vformat(format_string, args, kwargs, used_args, 2)
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/string.py", line 201, in _vformat
    self.parse(format_string):
  File "/home/miniconda3/envs/snakemake-tutorial/lib/python3.5/string.py", line 285, in parse
    return _string.formatter_parser(format_string)
TypeError: expected str, got list

谢谢您的帮助

Answer 1

您在这里不使用通配符。

您的规则fastqc_generate_qc将所有fastq文件作为输入并在此处输出所有fastqc文件。在蛇制作中要记住的一件事是：expand产生文件列表。您不想在这里：

rule fastqc_generate_qc:
    input:
        FASTQDIR + "{sample}.fastq.gz"
    output:
        WDIR + "Fastqc/{sample}_fastqc.html",
        WDIR + "Fastqc/{sample}_fastqc.zip"
    shell:
        "fastqc --outdir Fastqc/ {input}"

这里sample是通配符。这是您的全部规则，将触发实际文件名的产生。然后，规则fastqc_generate_qc将使用通配符将规则应用于规则all中要求的任何输出。

有关信息，如果要在扩展功能中使用通配符，则必须加括号：expand("path/{{study}}/{sample}, sample=SAMPLES)在这里，study是通配符，sample不是通配符。 sample值在扩展函数的第二个参数中定义。