Can publishDir in be dynamically set based on input type?

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1

Hi,

I’m working on a Nextflow pipeline and I’m trying to figure out if it’s possible to dynamically set the publishDir for outputs based on the input type. Specifically, I have a process that I use twice for both case and control as a tuple of values and paths, and I want the output to be published to different directories depending on one of the values in the tuple.

Here’s a simplified version of the process I’m working with:

#!/usr/bin/env nextflow

process tupled_data {
    publishDir "/home/zeddafir/scripts/nextflow/test_next/case", mode: 'copy', overwrite: true
    publishDir "/home/zeddafir/scripts/nextflow/test_next/control", mode: 'copy', overwrite: true

    input:
    tuple val(sampleName), path(samplePath), val(sampleType)

    output:
    path(path("${sampleName}.txt"))

    script:
    """
    echo "${sampleName} content" > ${sampleName}.txt
    """
}
2

If sampleType is your case or control you could use try something like this:

#!/usr/bin/env nextflow

process tupled_data {
    publishDir "/home/zeddafir/scripts/nextflow/test_next/${sampleType}", mode: 'copy', overwrite: true

    input:
    tuple val(sampleName), path(samplePath), val(sampleType)

    output:
    path(path("${sampleName}.txt"))

    script:
    """
    echo "${sampleName} content" > ${sampleName}.txt
    """
}