Snakemake InputFunctionException. AttributeError: 'Wildcards' object has no attribute

Question

我有一个带有 ChIP-seq 单端 fastq 文件名的列表对象 allfiles=['/path/file1.fastq','/path/file2.fastq','/path/file3.fastq']。我正在尝试将该对象 allfiles 设置为通配符（我想要 fastqc 规则的输入（以及映射等其他规则，但让我们保持简单）。我尝试了下面代码中的内容(lambda wildcards: data.loc[(wildcards.sample),'read1'])。但是，这给了我错误

"InputFunctionException in line 118 of Snakefile:
AttributeError: 'Wildcards' object has no attribute 'sample'
Wildcards:
"

有人知道具体怎么定义吗？看起来我很接近，我得到了一般的想法，但我没有得到正确的语法并执行它。谢谢！

代码：

import pandas as pd
import numpy as np

# Read in config file parameters
configfile: 'config.yaml'
sampleFile = config['samples'] # three columns: sample ID , /path/to/chipseq_file_SE.fastq , /path/to/chipseq_input.fastq
outputDir = config['outputdir'] # output directory

outDir = outputDir + "/MyExperiment"
qcDir = outDir + "/QC"

# Read in the samples table
data = pd.read_csv(sampleFile, header=0, names=['sample', 'read1', 'inputs']).set_index('sample', drop=False)
samples = data['sample'].unique().tolist() # sample IDs
read1 = data['read1'].unique().tolist() # ChIP-treatment file single-end file
inplist= data['inputs'].unique().tolist() # the ChIP-input files
inplistUni= data['inputs'].unique().tolist() # the ChIP-input files (unique)
allfiles = read1 + inplistUni

# Target rule
rule all:
    input:
        expand(f'{qcDir}' + '/raw/{sample}_fastqc.html', sample=samples),
        expand(f'{qcDir}' + '/raw/{sample}_fastqc.zip', sample=samples),

# fastqc report generation
rule fastqc:
    input: lambda wildcards: data.loc[(wildcards.sample), 'read1']
    output:
        html=expand(f'{qcDir}' + '/raw/{sample}_fastqc.html',sample=samples) ,
        zip=expand(f'{qcDir}' + '/raw/{sample}_fastqc.zip',sample=samples)
    log: expand(f'{logDir}' + '/qc/{sample}_fastqc_raw.log',sample=samples)
    threads: 4
    wrapper: "fastqc {input} 2>> {log}"

Answer 1

目前 rule fastqc 的 output 个文件在解析后没有任何通配符。也就是说，当前在 snakefile 中有一项作业 rule fastqc 尝试为所有样本生成一个输出文件。

但是，您似乎想运行 rule fastqc 分别为每个样本。在这种情况下，它需要概括如下，其中 {sample} 是通配符：

rule fastqc:
    input: lambda wildcards: data.loc[(wildcards.sample), 'read1']
    output:
        html = qcDir + '/raw/{sample}_fastqc.html,
        zip=qcDir + '/raw/{sample}_fastqc.zip'
    log: logDir + '/qc/{sample}_fastqc_raw.log'
    threads: 4
    shell: "fastqc {input} 2>> {log}"

Snakemake InputFunctionException. AttributeError: 'Wildcards' object has no attribute

Snakemake InputFunctionException. AttributeError: 'Wildcards' object has no attribute

wildcard

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