nextflow.config

/*___________________________________________________

             Nextflow DSL2 Main Config

  Author(s): Anuj Srivastava, Carolyn Paisie, Barry Guglielmo, Michael Lloyd, Brian Sanderson, Sai Lek
       Copyright of Jackson Laboratories 2022

_____________________________________________________*/

params {
    // Select workflow
    workflow = 'stitch'

    // 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
includeConfig params.config

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

manifest {
    name = "The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines"
    homePage = "https://github.com/TheJacksonLaboratory/cs-nf-pipelines"
    mainScript = "main.nf"
    nextflowVersion = "!>=20.10.0"
    version = "0.2.0"
}

profiles {
    sumner       { includeConfig "config/profiles/sumner.config" }
    elion        { includeConfig "config/profiles/elion.config" }
    sumner2      { includeConfig "config/profiles/sumner2.config" }
}

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