Basic pipeline

This example shows how to write a pipeline with two simple Bash processes, so that the results produced by the first process are consumed by the second process. 

#!/usr/bin/env nextflow

params.in = "$baseDir/data/sample.fa"

/*
 * Split a fasta file into multiple files
 */
process splitSequences {

    input:
    path 'input.fa'

    output:
    path 'seq_*'

    """
    awk '/^>/{f="seq_"++d} {print > f}' < input.fa
    """
}

/*
 * Reverse the sequences
 */
process reverse {

    input:
    path x

    output:
    stdout

    """
    cat $x | rev
    """
}

/*
 * Define the workflow
 */
workflow {
    splitSequences(params.in) \
      | reverse \
      | view
}

Synopsis