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I have the following Nextflow script:

nextflow.enable.dsl=2
include { check_folders; downloadClinvar; downloadReferenceGenome; downloadBedFiles; downloadGatkVcfFiles } from '/home/user/Desktop/pipeline/download_data.nf'
workflow {
    check_folders()
    downloadClinvar(check_folders.out)
    downloadReferenceGenome(check_folders.out)
    downloadBedFiles(check_folders.out)
    downloadGatkVcfFiles(check_folders.out)
}

The graph that is generated for me using the -preview -with-dag flags is the following: enter image description here

When I run the workflow it works fine but it performs each step sequentially, and I want it to download everything at the same time.

What could be happening to me? Why is my nextflow script executed sequentially?

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  • $\begingroup$ Cross-postd stackoverflow.com/questions/78445082/… $\endgroup$
    – ATpoint
    Commented May 8 at 8:34
  • 1
    $\begingroup$ Does the machine you run on have sufficient resources to run these processes in parallell? $\endgroup$
    – Pallie
    Commented May 8 at 14:19
  • $\begingroup$ Yes Pallie, I have Intel i8 7th generation, with 16GB of RAM $\endgroup$ Commented May 9 at 10:20
  • $\begingroup$ If your processes request a large amount of RAM/processors per process, that still could be the reason you're not getting parallellised processes $\endgroup$
    – Pallie
    Commented May 14 at 8:40

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