nextflow.config

manifest {
  author = 'Dan Fornika'
  name = 'BCCDC-PHL/dragonflye-nf'
  version = '0.1.3'
  description = 'Nextflow wrapper for Dragonflye Assembler'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.01.0'
}

params {
  prokka = false
  bakta = false
  hybrid = false
  long_only = false
  use_unicycler_circularization_tag = false
  rotate_replicons = false
  start_genes = "${baseDir}/assets/start_genes.fa"
  bakta_db = '/data/ref_databases/bakta/latest'
  illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
  long_read_suffixes = ['*_RL', '*_L']
  fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
  fastq_search_path = makeFastqSearchPath(illumina_suffixes, fastq_exts)
  fastq_input = 'NO_FILE'
  long_reads_search_path = makeLongReadsSearchPath(long_read_suffixes, fastq_exts)
  fastq_input_long = 'NO_FILE'
  filtlong_min_length = 1000
  filtlong_keep_percent = 90
  flye_meta = false
  samplesheet_input = 'NO_FILE'
  versioned_outdir = false
  collect_outputs = false
  collected_outputs_prefix = 'collected'
  pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
  pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
}

def makeFastqSearchPath(illumina_suffixes, fastq_exts) {
    def fastq_search_path = []
    if (params.fastq_input.toString() != 'NO_FILE') {
        for (suffix in illumina_suffixes) {
            for (ext in fastq_exts) {
                fastq_search_path.add(params.fastq_input.toString() + '/' + suffix.toString() + ext.toString())
            }
	}
    }
    return fastq_search_path
}

def makeLongReadsSearchPath(long_read_suffixes, fastq_exts) {
    def fastq_search_path = []
    if (params.fastq_input_long.toString() != 'NO_FILE') {
        for (suffix in long_read_suffixes) {
            for (ext in fastq_exts) {
                fastq_search_path.add(params.fastq_input_long.toString() + '/' + suffix.toString() + ext.toString())
	    }
        }
    }
    return fastq_search_path
}

def parseMinorVersion(version) {
    minor_version = version.split('\\.')[0..1].join('.')
    return minor_version
}

def parsePipelineName(name) {
    short_name = name.split('/')[1]
    return short_name
}

profiles {
  conda {
    process.conda = "$baseDir/environments/environment.yml"
    if (params.cache){
     conda.cacheDir = params.cache
    }
  }
}


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

process {
  withName: quast {
    cpus = 2
  }
  withName: fastp {
    cpus = 4
  }
  withName: filtlong {
    cpus = 12
  }
  withName: dragonflye {
    cpus = 12
    conda = "$baseDir/environments/dragonflye.yml"
  }
  withName: rotate_replicons {
    cpus = 8
  }
  withName: prokka {
    cpus = 8
  }
  withName: bakta {
    cpus = 12
    conda = "$baseDir/environments/bakta.yml"
  }
}