[英]Snakemake not recognizing multiple files as input
I'm having some trouble running snakemake.我在运行 snakemake 时遇到了一些问题。 I want to perform quality control of some RNA-Seq bulk samples using FastQC.
我想使用 FastQC 对一些 RNA-Seq 批量样本进行质量控制。 I've written the code in a way that all files following the pattern
{sample}_{replicate}.fastq.gz
should be used as input, where {sample}
is the sample id (ie SRR6974023) and {replicate}
is 1 or 2. My little scripts follows:我编写代码的方式是,所有遵循模式
{sample}_{replicate}.fastq.gz
的文件都应该用作输入,其中{sample}
是样本 id(即 SRR6974023), {replicate}
是 1或 2. 我的小脚本如下:
configfile: "config.yaml"
rule all:
input:
expand("raw_qc/{sample}_{replicate}_fastqc.{extension}", sample=config["samples"], replicate=[1, 2], extension=["zip", "html"])
rule fastqc:
input:
rawread=expand("raw_data/{sample}_{replicate}.fastq.gz", sample=config["samples"], replicate=[1, 2])
output:
compress=expand("raw_qc/{sample}_{replicate}_fastqc.zip", sample=config["samples"], replicate=[1, 2]),
net=expand("raw_qc/{sample}_{replicate}_fastqc.html", sample=config["samples"], replicate=[1, 2])
threads:
8
params:
path="raw_qc/"
shell:
"fastqc -t {threads} {input.rawread} -o {params.path}"
Just is case, the config.yaml
is:就是这样,
config.yaml
是:
samples:
SRR6974023
SRR6974024
The raw_data
directory with my files look like this:我的文件的
raw_data
目录如下所示:
SRR6974023_1.fastq.gz SRR6974023_2.fastq.gz SRR6974024_1.fastq.gz SRR6974024_2.fastq.gz
Finally, when I run the script, I always see the same error:最后,当我运行脚本时,我总是看到同样的错误:
Building DAG of jobs...
MissingInputException in line 8 of /home/user/path/Snakefile:
Missing input files for rule fastqc:
raw_data/SRR6974023 SRR6974024_2.fastq.gz
raw_data/SRR6974023 SRR6974024_1.fastq.gz
It see correctly only the last files, in this case SRR6974024_1.fastq.gz
and SRR6974024_2.fastq.gz
.它只正确看到最后一个文件,在这种情况下
SRR6974024_1.fastq.gz
和SRR6974024_2.fastq.gz
。 Whatsoever, the other one it's only seen as SRR6974023
.无论如何,另一个它只被视为
SRR6974023
。 How can I solve this issue?我该如何解决这个问题? I appreciate some help.
我很感激一些帮助。 Thank you all!
谢谢你们!
The yaml
is not configured correctly. yaml
配置不正确。 It should have -
to turn each row into a list:它应该
-
将每一行变成一个列表:
samples:
- SRR6974023
- SRR6974024
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