#!/usr/bin/env nextflow



/*
========================================================================================
    Workflow parameters are written as params.<parameter>
    and can be initialised using the `=` operator.
========================================================================================
*/

params.input = "data/yeast/reads/ref1_1.fq.gz"


ch1 = Channel.value( 'GRCh38' )
ch2 = Channel.value( ['chr1', 'chr2', 'chr3', 'chr4', 'chr5'] )
ch3 = Channel.value( ['chr1' : 248956422, 'chr2' : 242193529, 'chr3' : 198295559] )
ch1.view()
ch2.view()
ch3.view()

/*
========================================================================================
    Input data is received through channels
========================================================================================
*/

input_ch = Channel.fromPath(params.input)

/*
========================================================================================
   Main Workflow
========================================================================================
*/

workflow {
    //  The script to execute is called by it's process name, and input is provided between brackets.

    NUM_LINES(input_ch)

    /*  Process output is accessed using the `out` channel.
        The channel operator view() is used to print process output to the terminal. */

    NUM_LINES.out.view()

}

/*
========================================================================================
    A Nextflow process block. Process names are written, by convention, in uppercase.
    This convention is used to enhance workflow readability.
========================================================================================
*/
process NUM_LINES {

    input:
    path read

    output:
    stdout

    script:
    """
    # Print file name
    printf '${read}\\t'

    # Unzip file and count number of lines
    gunzip -c ${read} | wc -l
    """
}