nextflow.config

// params section used by all pipelines, othewrwise params are defined in the corresponding config files

params {

    // output
    OUTPUT_DIR          = "${launchDir}/results"
    
    // input cisbp data
    INPUT_DIR           = "${baseDir}/data"

    // section for variable used to check if the specific profile of each pipeline have been given by command line
    // add here the variables controlling this behaviour for the varius pipelines set them to false and
    // in the corresponding config file set them again to true

    GIVEN_JASPAR_PROFILE= false


    // for help messages, when --help is passed from command line
    help = false
}



profiles {

    test        {includeConfig "./conf/test.config"}
    crg         {includeConfig "./conf/crg.config"}
    bovreg      {includeConfig "./conf/bovreg.config"}
    err_strat   {includeConfig "./conf/error_strat.config"}
    gpu         {includeConfig "./conf/gpu.config"}
    singularity {includeConfig "./conf/singularity.config"}
    tower      	{includeConfig "./conf/tower.config"}
    sr_jaspar	{includeConfig "./conf/sr_jaspar.config"}
    unip_sparql {includeConfig "./conf/uniprot_sparql_query.config"}

}