我对Snakemaker非常陌生，也不太会说Python(抱歉，这可能是一个非常基本的愚蠢问题)：

我目前正在构建一个管道来使用atlas分析一组bamfile。这些bamfile位于不同的文件夹中，不应移动到公共文件夹中。因此，我决定提供一个示例列表，如下所示(这只是一个示例，实际上示例可能位于完全不同的驱动器上)：

Sample     Path
Sample1    /some/path/to/my/sample/
Sample2    /some/different/path/

并使用：

sample_file: /path/to/samplelist/samplslist.txt

现在转到我的Snakefile：

import pandas as pd

#define configfile with paths etc.
configfile: "config.yaml"

#read-in dataframe and define Sample and Path
SAMPLES = pd.read_table(config["sample_file"])
BAMFILE = SAMPLES["Sample"]
PATH = SAMPLES["Path"]

rule all:
    input:
        expand("{path}{sample}.summary.txt", zip, path=PATH, sample=BAMFILE)

#this works like a charm as long as I give the zip-function in the rules 'all' and 'summary':

rule indexBam:
    input: 
        "{path}{sample}.bam"
    output:
        "{path}{sample}.bam.bai"
    shell:
        "samtools index {input}"

#this following command works as long as I give the specific folder for a sample instead of {path}.
rule bamdiagnostics:
    input:
        bam="{path}{sample}.bam",
        bai=expand("{path}{sample}.bam.bai", zip, path=PATH, sample=BAMFILE)
    params:
        prefix="analysis/BAMDiagnostics/{sample}"   
    output:
        "analysis/BAMDiagnostics/{sample}_approximateDepth.txt",
        "analysis/BAMDiagnostics/{sample}_fragmentStats.txt",
        "analysis/BAMDiagnostics/{sample}_MQ.txt",
        "analysis/BAMDiagnostics/{sample}_readLength.txt",
        "analysis/BAMDiagnostics/{sample}_BamDiagnostics.log"
    message:
        "running BamDiagnostics...{wildcards.sample}"
    shell:
        "{config[atlas]} task=BAMDiagnostics bam={input.bam} out={params.prefix} logFile={params.prefix}_BamDiagnostics.log verbose"

rule summary:
    input:
        index=expand("{path}{sample}.bam.bai", zip, path=PATH, sample=BAMFILE),
        bamd=expand("analysis/BAMDiagnostics/{sample}_approximateDepth.txt", sample=BAMFILE)
    output:
        "{path}{sample}.summary.txt"
    shell:
        "echo -e '{input.index} {input.bamd}"

我收到错误

有人能帮我吗？ -我试图用join或创建输入函数来解决这个问题，但我认为我只是不够熟练，无法看到我的错误... -我猜问题是，我的摘要规则不包含带有bam诊断-输出{path}的Tuplet(因为输出在其他地方)，并且无法连接到输入文件或更多... -扩展我对bamtugstics的输入-规则使代码正常工作，但当然，将每个样本输入到每个样本输出，并造成巨大的混乱： In this case, both bamfiles are used for the creation of each outputfile. This is wrong as the samples AND the output are to be treated independently.

推荐答案

根据图集文档，您似乎需要为每个样本分别运行每个规则，这里的复杂之处在于每个样本位于不同的路径中。

import pandas as pd
from pathlib import Path

df = pd.read_csv('sample.tsv', sep='	', index_col='Sample')
SAMPLES = df.index
BAM_PATH = df["Path"]
# print (BAM_PATH['sample1'])

rule all:
    input:
        expand("{path}{sample}.summary.txt", zip, path=BAM_PATH, sample=SAMPLES)


rule indexBam:
    input:
        str( Path("{path}") / "{sample}.bam")
    output:
        str( Path("{path}") / "{sample}.bam.bai")
    shell:
        "samtools index {input}"

#this following command works as long as I give the specific folder for a sample instead of {path}.
rule bamdiagnostics:
    input:
        bam = lambda wildcards: str( Path(BAM_PATH[wildcards.sample]) / f"{wildcards.sample}.bam"),
        bai = lambda wildcards: str( Path(BAM_PATH[wildcards.sample]) / f"{wildcards.sample}.bam.bai"),
    params:
        prefix="analysis/BAMDiagnostics/{sample}"
    output:
        "analysis/BAMDiagnostics/{sample}_approximateDepth.txt",
        "analysis/BAMDiagnostics/{sample}_fragmentStats.txt",
        "analysis/BAMDiagnostics/{sample}_MQ.txt",
        "analysis/BAMDiagnostics/{sample}_readLength.txt",
        "analysis/BAMDiagnostics/{sample}_BamDiagnostics.log"
    message:
        "running BamDiagnostics...{wildcards.sample}"
    shell:
        ".atlas task=BAMDiagnostics bam={input.bam} out={params.prefix} logFile={params.prefix}_BamDiagnostics.log verbose"

rule summary:
    input:
        bamd = "analysis/BAMDiagnostics/{sample}_approximateDepth.txt",
        index = lambda wildcards: str( Path(BAM_PATH[wildcards.sample]) / f"{wildcards.sample}.bam.bai"),
    output:
        str( Path("{path}") / "{sample}.summary.txt")
    shell:
        "echo -e '{input.index} {input.bamd}"