Nextflow Units file specified is not found. Please provide a valid file.

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英文:

Nextflow Units file specified is not found. Please provide a valid file

问题

以下是您提供的内容的翻译:

我有以下的 Nextflow 脚本,它在下面提到的目录中运行工具 perf,对所有分割的 fastq 文件进行处理。当我运行脚本时,我收到以下错误:

    * 执行进程时发生错误 > 'perf (29)'
     原因是:
     进程 'perf (29)' 以错误的退出状态 (1) 终止
     执行的命令:
     /proj/perf/bin/PERF -i Condition_R1paired.part_016.fastq -o Condition_R1paired.part_016.tsv --格式 fastq -m 1 -M 6 -u repeat_units.txt
     命令退出状态:
      1
     命令输出:
     (空)
     命令错误:
     指定的单位文件不存在。请提供有效的文件
     工作目录:
     /proj/perf/work/57/c9208b00b8c5c82c3f1fdf6c7d0f07
    *提示: 通过切换到进程工作目录并显示名为 `.command.sh` 的脚本文件,您可以尝试找出问题在哪里**

这是脚本

    params.fastq_dir = "/proj/split_fastq/*.fastq";

    params.outdir = '/proj/work/output';

    fastq_file_index=Channel.fromPath(params.fastq_dir, checkIfExists: true ).map { it -> [it.baseName, it] }

    process perf {
   
    publishDir("${params.outdir}", mode: 'copy')
   
    输入:
	tuple val(file_name), path(fastq_file)
    
    输出:
    path "${file_name}.tsv"
   
    
    脚本:
    """
    /proj/perf/bin/PERF -i ${fastq_file} -o ${file_name}.tsv --格式 fastq -m 1 -M 6 -u repeat_units.txt

    """
  
     }


    工作流程 {
   
        perf(fastq_file_index).view()
   
     }

对于疑似错误和潜在修复的任何提示都欢迎,我猜测 repeat_units.txt 无法与所有 Nextflow 进程同时共享?如果是这样,如何将一个文件与多个进程共享?此外,欢迎提供改进代码的任何指针,因为我是 Nextflow 的新手。谢谢

希望这有助于您理解您的脚本和错误信息。如果您需要进一步的帮助,请随时提问。

英文:

I have a following nextflow script which runs a tool perf on all the split fastq files located in the below mentioned directory. When I run the script I get the following error:

*Error executing process > 'perf (29)'
 Caused by:
 Process `perf (29)` terminated with an error exit status (1)
 Command executed:
 /proj/perf/bin/PERF -i Condition_R1paired.part_016.fastq -o Condition_R1paired.part_016.tsv --format fastq -m 1 -M 6 -u repeat_units.txt
 Command exit status:
  1
 Command output:
 (empty)
 Command error:
 Units file specified is not found. Please provide a valid file
 Work dir:
 /proj/perf/work/57/c9208b00b8c5c82c3f1fdf6c7d0f07
*Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script* file named `.command.sh`**

This is the script

params.fastq_dir = "/proj/split_fastq/*.fastq"

params.outdir = '/proj/work/output'

fastq_file_index=Channel.fromPath(params.fastq_dir, checkIfExists: true ).map { it -> [it.baseName, it] }

process perf {

publishDir("${params.outdir}", mode: 'copy')

input:
tuple val(file_name), path(fastq_file)

output:
path "${file_name}.tsv"


script:
"""
/proj/perf/bin/PERF -i ${fastq_file} -o ${file_name}.tsv --format fastq -m 1 -M 6 -u repeat_units.txt

"""

 }


workflow {

    perf(fastq_file_index).view()

 }

Any tip on suspected error and potential fix is welcome, I am guessing the repeat_units.txt cannot be shared concurrently with all the nextflow processes? In that case how do I share a file with multiple processes? Also any pointers on improving the code is welcome as I am new to nextflow. Thanks

答案1

得分: 1

这实际上不是一个Nextflow错误。PERF 只是要求您提供一个单位文件:

未找到指定的单位文件。请提供一个有效的文件

一种方法是使用额外的参数来指定文件。然后,可以使用value通道将该文件传递给每个进程。请注意,当使用一个简单的值来调用进程时,该值通道会被隐式创建<sup>1</sup>。您可以尝试以下方法:

params.repeat_units = '/path/to/repeat_units.txt'

params.outdir = './results'

    publishDir "${params.outdir}/perf", mode: 'copy'

    input:
    tuple val(sample_name), path(fastq_file)
    path repeat_units

    output:
    tuple val(sample_name), path("${sample_name}.tsv")

    """
    PERF \\
        -i "${fastq_file}" \\
        -o "${sample_name}.tsv" \\
        --format fastq \\
        -m 1 \\
        -M 6 \\
        -u "${repeat_units}"
    """
}

    Channel
        .fromPath( params.fastq_files, checkIfExists: true )
        .map { tuple( it.baseName, it ) }
        .set { fastq_files }

    repeat_units = file( params.repeat_units )

    perf( fastq_files, repeat_units )
 }
英文:

This is not a Nextflow error per se. PERF is just asking you to provide a units file:

> Units file specified is not found. Please provide a valid file

One way would be to use an extra parameter to specify the file. The file could then be passed to each of the processes using a value channel. Note that a value channel is implicitly created by a process when it is invoked with a simple value<sup>1</sup>. You could try the following:

params.fastq_files = &quot;/proj/split_fastq/*.fastq&quot;
params.repeat_units = &#39;/path/to/repeat_units.txt&#39;

params.outdir = &#39;./results&#39;
process perf {

    publishDir &quot;${params.outdir}/perf&quot;, mode: &#39;copy&#39;

    input:
    tuple val(sample_name), path(fastq_file)
    path repeat_units

    output:
    tuple val(sample_name), path(&quot;${sample_name}.tsv&quot;)

    &quot;&quot;&quot;
    PERF \\
        -i &quot;${fastq_file}&quot; \\
        -o &quot;${sample_name}.tsv&quot; \\
        --format fastq \\
        -m 1 \\
        -M 6 \\
        -u &quot;${repeat_units}&quot;
    &quot;&quot;&quot;

}
workflow {

    Channel
        .fromPath( params.fastq_files, checkIfExists: true )
        .map { tuple( it.baseName, it ) }
        .set { fastq_files }

    repeat_units = file( params.repeat_units )

    perf( fastq_files, repeat_units )
 }

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  • 本文由 发表于 2023年3月7日 05:16:30
  • 转载请务必保留本文链接:https://go.coder-hub.com/75655927.html
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