Publication behaviour example

main.nf

#!/usr/bin/env nextflow

params.outdir = 'results'
params.all = false

workflow {
    First()

    First.out.value | Second
    Second.out.value | Third
}


process First {
    publishDir params.outdir
    container 'quay.io/nextflow/bash'
    output:
    val(1), emit: value
    path('*'), emit: files
    
    script:
    makeAll = params.all ? "echo 1 > my-folder/all.txt" : ""
    """
    mkdir -p my-folder/subfolder1/subsub
    ${makeAll}
    echo 1 > my-folder/subfolder1/1.txt
    """
}

process Second {
    publishDir params.outdir
    container 'quay.io/nextflow/bash'

    input:
    val(x)

    output: 
    val(x), emit: value
    path('*'), emit: files

    script:
    makeAll = params.all ? "echo 12 > my-folder/all.txt" : ""
    """
    mkdir -p my-folder/subfolder2/subsub
    ${makeAll}
    echo 2 > my-folder/subfolder2/2.txt
    """
}

process Third {
    publishDir params.outdir
    container 'quay.io/nextflow/bash'

    input:
    val(x)
    
    output:
    path('*')
    
    script:
    makeAll = params.all ? "echo 123 > my-folder/all.txt" : ""
    """
    mkdir -p my-folder/subfolder3/subsub
    ${makeAll}
    echo 3 > my-folder/subfolder3/3.txt
    """
}