nextflow.config

/*
                    fmalmeida/ngs-preprocess pipeline configuration file

                    Maintained by Felipe Marques de Almeida
                    Contact: almeidafmarques@outlook.com
 */
// Load base.config (contains some label resources configurarion)
includeConfig 'conf/base.config'

// loading required / default pipeline parameters
includeConfig 'conf/defaults.config'

// Nextflow management
params {

  // Boilerplate options
    help                       = false
    get_config                 = false
    validate_params            = true
    schema_ignore_params       = ''
    show_hidden_params         = false
  
  // Config options
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null

}

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

/*
                                    Setting up NF profiles
                            To use different profiles and executors
            please read more at: https://www.nextflow.io/docs/latest/config.html#config-profiles
 */
profiles {

  // load profiles
  standard    { includeConfig 'conf/standard.config'    }
  conda       { includeConfig 'conf/conda.config'       }
  docker      { includeConfig 'conf/docker.config'      }
  singularity { includeConfig 'conf/singularity.config' }
  test        { includeConfig 'conf/test.config'        }

}

/*


                      Configuring Nextflow Scopes.

                      Enable or not the production of Nextflow Reports


 */
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
// Trace Report
trace {
    enabled = true      // Enable? true or false
    file = "${params.output}/pipeline_info/ngs_preprocess_tracing_${trace_timestamp}.txt"
    fields = 'task_id,name,status,exit,realtime,cpus,%cpu,memory,%mem,rss'
}

// Timeline Report
timeline {
    enabled = true      // Enable? true or false
    file = "${params.output}/pipeline_info/ngs_preprocess_timeline_${trace_timestamp}.html"
}

// Complete Report
report {
    enabled = true      // Enable? true or false
    file = "${params.output}/pipeline_info/ngs_preprocess_report_${trace_timestamp}.html"
}

/*
                                    Adding manifest
*/
manifest {
  name            = "fmalmeida/ngs-preprocess"
  author          = "Felipe Almeida"
  description     = "Nextflow pipeline for NGS preprocessing"
  homePage        = "https://github.com/fmalmeida/ngs-preprocess"
  mainScript      = "main.nf"
  nextflowVersion = ">=21.10.0"
  version         = "2.7.1"
}