nextflow.config

params {
    // set workflow
    pipeline = 'Not_Specified'
    workflow = params.pipeline

    // define reference_cache directory
    reference_cache='/projects/omics_share'

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

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

    profile = 'sumner2'

    // 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
    fastq2 = true // default is PE for workflows
    tmpdir = "/flashscratch/${USER}"  // generic param
    merge_replicates = false
    // get help
    help = null

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

try {
    includeConfig params.config
} catch (Exception e) {
    System.err.println("ERROR: Could not load ${params.config} check that you are using a valid workflow name")
    System.exit(1)
}


// work directory is important as it will be large, plan accordingly
workDir = "/flashscratch/${USER}/${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 = "!>=22.04.3"
    version = "0.7.5"
    author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Tejas Temker, Anuj Srivastava. Copyright Jackson Laboratory 2024'
}


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

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

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

trace {
    enabled = true
    file = "${params.pubdir}/trace/trace_${trace_timestamp}.txt"
    overwrite = true
    fields = \
         "task_id,"   \
       + "hash,"      \
       + "process,"   \
       + "tag,"       \
       + "status,"    \
       + "exit,"      \
       + "start,"     \
       + "container," \
       + "cpus,"      \
       + "time,"      \
       + "disk,"      \
       + "memory,"    \
       + "duration,"  \
       + "realtime,"  \
       + "queue,"     \
       + "%cpu,"      \
       + "%mem,"      \
       + "rss,"       \
       + "peak_rss,"  \
       + "vmem,"      \
       + "peak_vmem," \
       + "rchar,"     \
       + "wchar"
}
 
dag {
    enabled = true
    file = "${params.pubdir}/trace/${params.workflow}_dagPlot_${trace_timestamp}.html"
    overwrite = true
}