nextflow.config

// #################################################### \\
// ~~~~~~~~~~~~~~~~ BASE CONFIGURATION ~~~~~~~~~~~~~~~~ \\

// Ensure DSL1 is used as DSL2 is the new default and version must be set after v23 release
nextflow.enable.dsl = 1
nextflow.version = '21.10.6'

manifest {
    name = 'MGP1000'
    author = 'Patrick Blaney'
    homePage = 'https://github.com/pblaney/mgp1000'
    description = 'Complete end-to-end modular pipeline for the large-scale collaborative analysis of Multiple Myeloma genomes'
    nextflowVersion = '>=20.01.0'
    version = '1.0'
}

// Set global default parameters used in config file that will be overwritten with CLI run command
params {
    run_id = null
    email = null
    cpus = null
    memory = null
    queue_size = 100
    executor = 'slurm'
}

// Load executor specific configuration layer
try {
    includeConfig "conf/${params.executor}.config"
} catch( Exception e ) {
    System.err.println("ERROR: Could not find specific config file for executor [${params.executor}] in conf/ directory")
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

notification {
    
    if( "${params.email}" ) {
        enabled = true
        to = "${params.email}"
        from = "${params.email}"
    } else {
        enabled = false
    }
}

report {
    enabled = true
    file = "nextflow_report.${params.run_id}.html"
}

timeline {
    enabled = true
    file = "timeline_report.${params.run_id}.html"
}

trace {
    enabled = true
    fields = "task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes"
    file = "trace.${params.run_id}.txt"
}

// #################################################### \\