nextflow.config

plugins { id 'nf-schema@2.2.0' }


manifest {
    name            = 'Lodestone'
    author          = """Anna Price, Tom Whalley, Arthur Morris"""
    homePage        = 'https://github.com/pathogen-genomics-cymru/lodestone'
    description     = """Genomic Sequencing pipeline for Mycobacterial isolates"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=20.0'
    version         = '0.9.9'
}

validation {
  help {
    enabled = true
  }
  // for now ignore parameters that are nested.
  ignoreParams = ["kraken","afanc","bowtie","resistance","resources"]
}


params {
  help = ""
  // do we proceed after decontamination if an error occurs?
  permissive = false

  // glob pattern for input files
  pattern = ""
  output_dir = ""
  input_dir = ""
  // filetype fastq or bam
  filetype = 'fastq'
  // unmix myco 'yes' or 'no'
  unmix_myco = false

  // principal species in each sample, assuming genus Mycobacterium, default null
  // otherwise takes 1 of 10 values: abscessus, africanum, avium, bovis, chelonae, chimaera, fortuitum, intracellulare, kansasii, tuberculosis
  species = 'null'

  // path to singularity recipes directory (needed to strip software versions in getversion)
  sing_dir = "${baseDir}/singularity"
  // path to this config file (needed to strip database versions in getversion)
  config_file = "${baseDir}/nextflow.config"

  //thresholds in kraken
  kraken {
    // % of reads needed to kept in kraken report and outright number of reads
    kraken_percent_threshold = 10
    kraken_n_reads_threshold = 10000
    kraken_db = "kraken2"
  }

  afanc {
    // as above
    afanc_percent_threshold = 5
    afanc_n_reads_threshold = 1000
      
    // If a failure happened, more permissive threshold
    afanc_fail_percent_threshold = 2
    afanc_fail_n_reads_threshold = 500
      
    afanc_myco_db = "${baseDir}/Mycobacteriaciae_DB_7.0/"
  }

  bowtie {
    bowtie_index = "bowtie2"
    bowtie_index_name = "hg19_1kgmaj"
  }

  resistance {
  // resistance params
  resistance_profiler = "tb-profiler"  
  collate = false
  }

  resources{
  resource_dir = "${baseDir}/resources"
  refseq = "${resource_dir}/assembly_summary_refseq.txt"
  }
}

process {
    withLabel:normal_cpu { cpus = 8 }
    withLabel:low_memory { memory = '5GB' }
    withLabel:medium_memory { memory = '10GB' }
    withLabel:high_memory { memory = '18GB' }
}

profiles {
    climb {
       includeConfig 'config/climb_k8s.config'
       includeConfig 'config/containers.config'
       
       process{        
        //add in docker configs as the above config file is generic for any containerised run
        docker.enabled = true
        fixOwnership = true
        runOptions = "-u \$(id -u):\$(id -g)"
        
        k8s {
           computeResourceType = 'Job'
        }    
        
        //params specific to paths on the climb system
        params{
          bowtie {
              bowtie2_index = "s3://microbial-bioin-sp3/bowtie_hg19"
              bowtie_index_name = "hg19_1kgmaj"
          }

          kraken {
              kraken_db = "s3://microbial-bioin-sp3/kraken_pluspf_16gb/"
          }

          afanc {
              afanc_myco_db = "s3://microbial-bioin-sp3/Mycobacteriaciae_DB_7.0/"
          }

          resources {
            resource_dir = "s3://microbial-bioin-sp3/lodestone_resources"
            refseq = "${resource_dir}/assembly_summary_refseq.txt"
          }        
      }
      
      
      withLabel:getversion{
       executor = "local"
       container = null
      }

      withLabel:afanc_parse{
       executor = "local"
       container = null
      }
    }
   }
    
    singularity {
        includeConfig 'config/containers.config'

        singularity.enabled = 'true'
        singularity.autoMounts = 'true'

        //path to the singularity containers
        singularity.cacheDir = "${baseDir}/singularity"

        //stop tmpdir stuff
        withLabel:new_tmp{
          env.SINGULARITY_TMPDIR = '${task.workDir}'
        }
    }

  sp3 {
  
    includeConfig 'config/containers.config'
    
    //add in singularity configs as the above config file is generic for any containerised run
    singularity.enabled = 'true'
    singularity.autoMounts = 'true'
    // path to the singularity containers
    singularity.cacheDir = "/data/images"

    process {
      scratch = true     
    }
 }


  docker {
    includeConfig 'config/containers.config'
    
    //add in docker configs as the above config file is generic for any containerised run
    docker.enabled = true
    fixOwnership = true
    runOptions = "-u \$(id -u):\$(id -g)"
  }
}