nextflow.config

/*
 * -------------------------------------------------
 *  Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

manifest {
  homePage = 'https://github.com/BU-ISCIII/bacterial_wgs_training'
  description = 'This is a project for wgs analysis trainning using nextflow and containers.'
  mainScript = 'main.nf'
}

// Global default params, used in configs
params {
  ver = '1.0' //Pipeline version
  nf_required_version = '0.27.6' //Minimum version of Nextflow required

  reads="$baseDir/data/samples/*.fastq.gz"
  outdir='results'
  step = "preprocessing"
  output_docs = "${baseDir}/docs/output.md"
  multiqc_config = "${baseDir}/conf/multiqc_config.yaml"
  // Mapping-duplicates defaults
  keepduplicates = false
  notrim = false
  outbreaker_config = false
  gtf = false
  bwa_index = false
  fasta = false
  cut_mean_quality = 20
  qualified_quality_phred = 20
  unqualified_percent_limit = 10
  min_trim_length = 50
  scheme = false
}

profiles {

  standard {
    includeConfig 'conf/base.config'
  }

  docker {
    includeConfig 'conf/docker.config'
  }

  singularity {
  	includeConfig 'conf/singularity.config'
  }

  conda {
	conda.enabled = true
	//conda.useMicromamba = true
    	//conda.channels = 'conda-forge,bioconda,defaults'
  	process{
  		// conda= "/opt/micromamba/envs/bacterial_wgs_training/"
  		withName:makeBWAindex {
    		conda = "/opt/micromamba/envs/bwa/"
  		}
  		withName:fastqc {
    		conda = "/opt/micromamba/envs/fastqc/"
  		}
  		withName:trimming {
    		conda = "/opt/micromamba/envs/fastp/"
  		}
  		withName:bwa {
    		conda = "/opt/micromamba/envs/bwa/"
  		}
  		withName:samtools {
    		conda = "/opt/micromamba/envs/mapping/"
  		}
  		withName:bwa_mapped {
    		conda = "/opt/micromamba/envs/mapping/"
  		}
  		withName:picard {
    		conda = "/opt/micromamba/envs/mapping/"
  		}
  		withName:unicycler {
    		conda = "/opt/micromamba/envs/unicycler/"
  		}
  		withName:quast {
    		conda = "/opt/micromamba/envs/quast/"
  		}
  		withName:prokka {
    		conda = "/opt/micromamba/envs/prokka/"
  		}
  		withName:snippy {
    		conda = "/opt/micromamba/envs/snippy/"
  		}
  		withName:snippy_core {
    		conda = "/opt/micromamba/envs/snippy/"
  		}
  		withName:gubbins {
    		conda = "/opt/micromamba/envs/snippy/"
  		}
  		withName:iqtree {
    		conda = "/opt/micromamba/envs/iqtree/"
  		}
  		withName:scheme_evaluation {
    		conda = "/opt/micromamba/envs/taranis/"
  		}
  		withName:taranis {
    		conda = "/opt/micromamba/envs/taranis/"
  		}
  		withName:plasmidid {
    		conda = "/opt/micromamba/envs/plasmidid/"
  		}
  		withName:srst2_virulence {
    		conda = "/opt/micromamba/envs/srst2/"
  		}
  		withName:srst2_mlst {
    		conda = "/opt/micromamba/envs/srst2/"
  		}
  		withName:srst2_serogroup {
    		conda = "/opt/micromamba/envs/srst2/"
  		}
  		withName:srst2_resistance {
    		conda = "/opt/micromamba/envs/srst2/"
  		}
  		withName:multiqc_preprocessing {
    		conda = "/opt/micromamba/envs/multiqc/"
  		}
  		withName:multiqc_mapping {
    		conda = "/opt/micromamba/envs/multiqc/"
  		}
  		withName:multiqc_assembly {
    		conda = "/opt/micromamba/envs/multiqc/"
  		}
  		withName:multiqc_outbreakSNP {
    		conda = "/opt/micromamba/envs/multiqc/"
  		}
  		withName:multiqc_preprocessing {
    		conda = "/opt/micromamba/envs/multiqc/"
  		}
    }
  }

  testing {
  	// TODO
  }

  aws {
  	// TO DO
  }

  none {
    // Don't load any config (for use with custom home configs)
  }

}

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

// By default output execution reports
timeline {
  enabled = true
  file = "${params.outdir}/timeline.html"
}
report {
  enabled = true
  file = "${params.outdir}/report.html"
}
trace {
  enabled = true
  file = "${params.outdir}/trace.txt"
}
dag {
  enabled = true
  file = "${params.outdir}/DAG.svg"
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
//def check_max(obj, type) {
//  if(type == 'memory'){
//    if(obj.compareTo(params.max_memory) == 1)
//      return params.max_memory
//    else
//      return obj
//  } else if(type == 'time'){
//    if(obj.compareTo(params.max_time) == 1)
//      return params.max_time
//    else
//      return obj
//  } else if(type == 'cpus'){
//    return Math.min( obj, params.max_cpus )
//  }
//}