DSL2 : use of the same channel multiple times in process

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Sylvain Brohee

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Mar 19, 2021, 6:19:12 AM3/19/21

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Dear list,

I have a trivial question. Hopefully, it has not been answered already.

In the process trimFastq hereafter, the channel scriptPath is emitted only once while the other the tuple should be emitted several times but it stopped at the first iteration of the process.

From the nextflow documentation, I understood that this can be solved by using value channel but with path channel, I don't know how to make the process run as many times as I have tuples emmitted.

I thank you a lot for your kind help,

Sylvain

Channel
               .fromPath(params.fastqDir + '/' +"*.fastq.gz")
               .map(path ->
                                            tuple(
                                                           (path.getBaseName() =~ /(.+)_S\d+_L00[1-4]_R[1-2]_001/)[0][1]
                                                           ,path
                                                           ,(path.getBaseName() =~ /.+_S\d+_(L00[1-4])_R[1-2]_001/)[0][1]
                                                           ,(path.getBaseName() =~ /.+_S\d+_L00[1-4]_(R[1-2])_001/)[0][1]
                                                           )
                              )
               .set{fastq_ch}


Channel.fromPath(params.scriptPath).set{scriptpath_ch}

// WORKFLOW

workflow {
               // for seqFF
               trimFastq(fastq_ch.dump(),scriptpath_ch)
}

process trimFastq {
               label 'env_pysam'
               label 'cpusmem_std'
               input:
                              tuple val(sampleName),path(inputFastq),val(lane),val(orientation)
                              path scriptPath
               output:
                              tuple val(sampleName),path("${sampleName}_${lane}_${orientation}_trim${params.trimLength}.fastq.gz"),val(lane),val(orientation)
               script:
                              """
                              python ${scriptPath}/shallow_cnv/trimFastqToLenght.py -z -l ${params.trimLength} \
                              -i ${inputFastq} -o ${sampleName}_${lane}_${orientation}_trim${params.trimLength}.fastq.gz
                              """
}

sylvain...@gmail.com

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Mar 19, 2021, 6:34:45 AM3/19/21

to Nextflow

I found the solution in the doc by re-reading carefully.

https://www.nextflow.io/docs/latest/process.html#process-understand-how-multiple-input-channels-work