ERROR ~ Cannot read write-only property: into - Looking for assistance with passing files from one process to a another

[PaddyKTaylor]

Within my workflow I'm wanting to make use of channels to have the file outputs from one process be the inputs for another process. I've attempted making use of inline into and from with my processes as well as an .out array in my workflow{}. Neither have been working and I receive an error message of:

 N E X T F L O W   ~  version 24.10.3

Launching `prototype_pipeline.nf` [scruffy_jepsen] DSL2 - revision: 35330007de

ERROR ~ Cannot read write-only property: into

I'm using version 24.10.3 and in my config file I've even added the following lines to ensure that DSL2 is used:

nextflow {
    enable {
        dsl = 2
    }
}

Here is some example dummy code based on what I'm trying to do with my workflow (I use the config file for variables and parameters):

process firstProcess {
    container dockerImage

    containerOptions = "-v \"${localDataDir}:/home/User\""

    publishDir "${analysisOutputDir}", mode: 'copy', pattern: 'firstProcessOutputDir/*'

    input:
    val initialFileInput

    output:
    path 'firstProcessOutput.bed' into bed_ch
    path 'firstProcessOutput.fam' into fam_ch
    path 'firstProcessOutput.bim' into bim_ch
    path 'firstProcessOutputDir/*'

    script:
    """
    [ ! -d "firstProcessOutputDir" ] && mkdir "firstProcessOutputDir"
    plink --file "${initialFileInput}" --make-bed --out firstProcessOutput
    plink --bfile firstProcessOutput --freq --hardy --missing --horse --out firstProcessOutputDir/finalOutputFile
    """
}

process secondProcess {
    container anotherDockerImage

    containerOptions = "-v \"${localDataDir}:/home/anotherUser\""

    publishDir "${analysisOutputDir}", mode: 'copy'

    input:
    path bed from bed_ch
    path fam from fam_ch
    path bim from bim_ch

    output:
    path 'finalAnalysis/*'
    
    script:
    """
    [ ! -d "finalAnalysis" ] && mkdir "finalAnalysis"
    king -b "${bed}" --fam "${fam}" --bim "${bim}" --ibdseg --prefix finalAnalysis/finalAnalysis
    """
}

workflow {
    firstProcess(initialFileInput)
    secondProcess()
}

Is there something fundamental about Nexflow syntax that I'm missing? Any assistance to better understand what's going on would be greatly appreciated.

[mribeirodantas]

from and into are DSL1 keywords. They've been discontinued for some time. I recommend this reading for converting your DSL1 code to DSL2 code. Also, for future questions, please ask them at https://community.seqera.io.