nextflow.config

/*___________________________________________________

             Nextflow DSL2 Main Config

  Authors: Brian J. Sanderson
       Copyright The University of Kansas 2023

_____________________________________________________*/

params {
    // Select workflow
    // workflow = 'rnaseq'

    // select config from config folder to use
    config = "config/${params.workflow}.config"

    // set publish directory for data to save (easier to follow)
    pubdir = "../${workflow}"

    // organize output:
    // by sample folders (with many analysis in one sample folder) or by
    // analysis folder (with many samples in one folder per analysis)

    organize_by = 'sample' // analysis
    keep_intermediate = false // true
    
    // get help
    help = null

    // make a comment for log
    comment = ''
}

// specific config for the pipeline


try {
    includeConfig params.config
} catch (Exception e) {
    System.err.println("ERROR: Could not load ${params.config} check that you are using a valid pipeline name")
}

// work directory is important as it will be large, plan accordingly
workDir = "/kuhpc/scratch/${USER}/${params.workflow}"

manifest {
    name = "KU-GDSC Nextflow Bioinformatics Workflows"
    homePage = "https://github.com/KU-GDSC/workflows"
    mainScript = "main.nf"
    nextflowVersion = "!>=20.10.0"
    version = "0.1.0"
}

profiles {
    gdsc    { includeConfig "config/profiles/gdsc.config" }
    kucg    { includeConfig "config/profiles/kucg.config" }
}

report {
    enabled = true
    file = "${params.pubdir}/${params.workflow}_report.html"
    overwrite = true
}

plugins {
    id 'nf-validation'
}