mock-dependency.adoc

Mock dependency

Problem

You need to synchronize the execution of two processes for which there isn’t a direct input-output relationship, so that process bar is executed only after the completion of process foo.

Solution

Add to the outputs of process foo a channel producing a flag value.

Then use this channel as input for process bar to trigger its execution when the other process completes.

Code

Channel
    .fromPath('.data/reads/*.fq.gz')
    .set{ reads_ch }

process foo {
    output:
    val true into done_ch

    script:
    """
    your_command_here
    """
}

process bar {
    input:
    val flag from done_ch
    file fq from reads_ch

    script:
    """
    other_commad_here --reads $fq
    """
}

Run it

Run the example using this command:

nextflow run patterns/mock-dependency.nf