How to reuse the same process twice in within the same module in nextflow dsl2, but saving the output in a different name?

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英文:

How to reuse the same process twice in within the same module in nextflow dsl2, but saving the output in a different name?

问题

以下是翻译好的部分:

"我正在构建一个Nextflow工作流(DSL2),在同一模块中,我需要两次重用相同的过程,但我使用的语法似乎让Nextflow感到不满意,因为它抱怨该过程已经被使用,并且需要正确地为其设置别名,问题是我不知道该如何做。

以下是错误消息:

'Process 'ReUsable' 已经被使用 - 如果您需要重用相同的组件,请使用不同的名称包括它,或者将其包含在不同的工作流上下文中'

以下是一个有意义的示例:

    publishDir "${params.publish_dir}/VF/SZ/${meta}", mode: 'copy', pattern: '*.out'
    container 'bla.1'
    input:
        tuple val(meta), path(input)
    output:
        tuple val(meta), path('one.out'), emit: out1
    script:
        """
        cat ${input} > one.out
        """
}
process ScndStep {
         publishDir "${params.publish_dir}/VF/${meta}", mode: 'copy', pattern: '*sub.out'
    container 'bla.2'
    input:
        tuple val(meta), path(out1)
    output:
        tuple val(meta), path('two.out'), emit: out2
    script:
        """
        sed -i "s/i/o/g" ${out1} > two.out
        """
}
workflow Unite {
      take:
               input
      main:
               out1 = ReUsable(input)
               out2 = ScndStep(out1)
               out3 = ReUsable(out2)
               .SaveAs{three.out}
      emit:
               out1
               out2
               out3

}

显然,这不是正确的方式,当我稍微查看了一下时,建议设置一个新模块,然后在其中两次包括ReUsable,每次使用不同的名称。然而,对我来说,这似乎过于复杂了。这里的整个重点是使它轻便,并在同一工作流中重用相同的过程,已经不得不重写一个ReUsable2过程超出了范围。有什么想法吗?非常感谢。"

英文:

i am building a nextflow workflow (DSL2) and within the same module i need to reuse the same process twice, but the syntax i am using seems to offend nextflow, in the sense that it complains that the process is already been used and i need to alias it properly, the thing is that i wouldn't know how.

Here is the error

Process 'ReUsable' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

and here a meaningful example:

process ReUsable {
    publishDir "${params.publish_dir}/VF/SZ/${meta}", mode: 'copy', pattern: '*.out'
    container 'bla.1'
    input:
        tuple val(meta), path(input)
    output:
        tuple val(meta), path('one.out'), emit: out1
    script:
        """
        cat ${input} > one.out
        """
}
process ScndStep {
         publishDir "${params.publish_dir}/VF/${meta}", mode: 'copy', pattern: '*sub.out'
    container 'bla.2'
    input:
        tuple val(meta), path(out1)
    output:
        tuple val(meta), path('two.out'), emit: out2
    script:
        """
        sed -i "s/i/o/g" ${out1} > two.out
        """
}
workflow Unite {
      take:
               input
      main:
               out1 = ReUsable(input)
               out2 = ScndStep(out1)
               out3 = ReUsable(out2)
               .SaveAs{three.out}
      emit:
               out1
               out2
               out3

}

Clearly this is not the correct way, and when i looked a bit around it was recommended to set up a new module to then include the ReUsable twice each time with different name. It seems to me however to overcomplicating things. The whole point here is to make it light and reuse the same process within the same workflow, already having to rewrite a ReUsable2 process is off the scope.
Any ideas?
Many thanks

答案1

得分: 1

是的 - 最简单的方法是使用include关键字。使用module aliases允许您重用具有相同名称的组件,例如:

main.nf的内容:

include { ReUsable as ReUsable1 } from './modules/reusable'
include { ReUsable as ReUsable2 } from './modules/reusable'
include { ScndStep } from './modules/secondstep'

workflow Unite {

      take:
      input_ch

      main:
      input_ch | ReUsable1 | ScndStep | ReUsable2

      emit:
      ReUsable1.out
      ScndStep.out
      ReUsable2.out
}

modules/reusable/main.nf的内容:

process ReUsable {

    input:
    tuple val(meta), path(input)

    output:
    tuple val(meta), path('one.out'), emit: out1

    script:
    """
    cat ${input} > one.out
    """
}

modules/secondstep/main.nf的内容:

process ScndStep {

    input:
    tuple val(meta), path(out1)

    output:
    tuple val(meta), path('two.out'), emit: out2

    script:
    """
    sed "s/i/o/g" ${out1} > two.out
    """
}

nextflow.config的内容:

params {

    publish_dir = './results'
}

process {

    withName: ReUsable1 {

        publishDir = [
            path: "${params.publish_dir}/ReUsable1",
            mode: 'copy',
        ]
    }

    withName: ScndStep {

        publishDir = [
            path: "${params.publish_dir}/ScndStep",
            mode: 'copy',
        ]
    }

    withName: ReUsable2 {

        publishDir = [
            path: "${params.publish_dir}/ReUsable2",
            mode: 'copy',
        ]
    }
}
英文:

Yes - the simplest approach is to use the include keyword for this. Using module aliases lets you reuse components with the same name, for example:

Contents of main.nf:

include { ReUsable as ReUsable1 } from './modules/reusable'
include { ReUsable as ReUsable2 } from './modules/reusable'
include { ScndStep } from './modules/secondstep'


workflow Unite {

      take:
      input_ch

      main:
      input_ch | ReUsable1 | ScndStep | ReUsable2

      emit:
      ReUsable1.out
      ScndStep.out
      ReUsable2.out
}

Contents of modules/reusable/main.nf:

process ReUsable {

    input:
    tuple val(meta), path(input)

    output:
    tuple val(meta), path('one.out'), emit: out1

    script:
    """
    cat ${input} > one.out
    """
}

Contents of modules/secondstep/main.nf:

process ScndStep {

    input:
    tuple val(meta), path(out1)

    output:
    tuple val(meta), path('two.out'), emit: out2

    script:
    """
    sed "s/i/o/g" ${out1} > two.out
    """
}

Contents of nextflow.config:

params {

    publish_dir = './results'
}

process {

    withName: ReUsable1 {

        publishDir = [
            path: "${params.publish_dir}/ReUsable1",
            mode: 'copy',
        ]
    }

    withName: ScndStep {

        publishDir = [
            path: "${params.publish_dir}/ScndStep",
            mode: 'copy',
        ]
    }

    withName: ReUsable2 {

        publishDir = [
            path: "${params.publish_dir}/ReUsable2",
            mode: 'copy',
        ]
    }
}

huangapple
  • 本文由 发表于 2023年7月20日 21:46:08
  • 转载请务必保留本文链接:https://go.coder-hub.com/76730547.html
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