snakemake：AmbiguousRuleException

Question

我正在尝试在snakemake中完成一个简单的管道，但是我不知道如何正确使用通配符。

我有一个包含以下文件的文件夹data：

• data/sample1_P1.txt

• data/sample1_P2.txt

• data/sample2_P1.txt

• data/sample2_P2.txt

此示例中的通配符为sampleX和PX。我要实现的是首先将文件移动到文件夹sample1和sample2中。

此步骤的期望输出：

• data/sample1/sample1_P1.txt

• data/sample1/sample1_P2.txt

• data/sample2/sample2_P1.txt

• data/sample2/sample2_P2.txt

下一步，我想将文件夹内的文件连接起来，生成文件：

• data/sample1/sample1_concatenated.txt

• data/sample2/sample2_concatenated.txt

这是我尝试过的：

pairs = {"P1" : "P1", "P2" : "P2"}

samples = {
    "sample1": "sample1",
    "sample2": "sample2"
}

rule all:
    input: expand("data/{sample}/{sample}_concatenated.txt", sample = samples)

rule get_txt_files:
    output:
        "data/{sample}_{pair}.txt"
    shell:
        """
        echo 1 > {output}
        """

rule reorganise:
  input:
    expand("data/{{sample}}_{pair}.txt", \
        pair=pairs)
  output:
    "data/{sample}/{sample}_{pair}.txt"
  shell:
    "mv {input} data/{wildcards.sample}/."

rule concat:
    input:
        expand("data/{{sample}}/{{sample}}_{pair}.txt", \
            pair=pairs)
    output:
        "data/{sample}/{sample}_concatenated.txt"
    shell:
        "cat {input} > {output}"

我收到一条错误消息AmbiguousRuleException，但我不知道如何解决此问题。

Answer 1

将以下内容添加到您的工作流程中：

wildcard_constraints:
    pair = "|".join(pairs),
    sample = "|".join(samples),

就像错误消息告诉您的一样，Snakemake找到了一种从两个不同规则产生输出的方法：

AmbiguousRuleException:
Rules reorganise and get_txt_files are ambiguous for the file data/sample1/sample1_concatenated.txt.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
    reorganise: pair=concatenated,sample=sample1
    get_txt_files: pair=concatenated,sample=sample1/sample1
Expected input files:
    reorganise: data/sample1_P1.txt data/sample1_P2.txt
    get_txt_files: Expected output files:
    reorganise: data/sample1/sample1_concatenated.txt
    get_txt_files: data/sample1/sample1_concatenated.txt

通过限制通配符，可以避免歧义。