nextflow.config

params {
  take = 1 //can be overwritten at run-time e.g. --take 2 to just process first two accessions or --take all to process all
  accessions = [
    "ACBarrie",
    "Alsen",
    "Baxter",
    "Chara",
    "Drysdale",
    "Excalibur",
    "Gladius",
    "H45",
    "Kukri",
    "Pastor",
    "RAC875",
    "Volcanii",
    "Westonia",
    "Wyalkatchem",
    "Xiaoyan",
    "Yitpi"
  ]

  adapters = "https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq3-PE.fa"

  ref {
    base_url = "https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v1.0/iwgsc_refseqv1.0_"
    chr      = "chr4A"
    start    = "688055092"
    end      = "688113092"
  }
  bam {
    base_url = "http://crobiad.agwine.adelaide.edu.au/dawn/jbrowse-prod/data/wheat_parts/minimap2_defaults/whole_genome/PE/BPA"
    chr      = "chr4A_part2"
    start    = "235500000"
    end      = "235558000"
  }
  outdir = "./results" //can be overwritten at run-time e.g. --outdir dirname
  infodir = "./flowinfo" //can be overwritten at run-time e.g. --infodir dirname
}

process {
  cache = 'lenient'
}

profiles {
  //SOFTWARE
  conda {
    process {
      conda = "$baseDir/conf/conda.yaml"
    }
  }
  condamodule {
    process.module = 'miniconda3/4.3.24'
  }
  docker {
    process.container = 'rsuchecki/nextflow-embl-abr-webinar'
    docker {
      enabled = true
      fixOwnership = true
    }
  }
  singularity {
    process {
      container = 'shub://csiro-crop-informatics/nextflow-embl-abr-webinar' //Singularity hub
      // container = 'rsuchecki/nextflow-embl-abr-webinar' //pulled from Docker hub - would suffice but Singularity container is re-built from docker image so not ideal for reproducibility
      //scratch = true //This is a hack needed for singularity versions approx after 2.5 and before 3.1.1 as a workaround for https://github.com/sylabs/singularity/issues/1469#issuecomment-469129088
    }
    singularity {
      enabled = true
      autoMounts = true
      cacheDir = "singularity-images"  //when distibuting the pipeline probably should point under $workDir
    }
  }
  singularitymodule {
    process.module = 'singularity/3.2.1' //Specific to our cluster - update as required
  }
  //EXECUTORS
  awsbatch {
    aws.region = 'ap-southeast-2'
    process {
      executor = 'awsbatch'
      queue = 'flowq'
      process.container = 'rsuchecki/nextflow-embl-abr-webinar'
    }
    executor {
      awscli = '/home/ec2-user/miniconda/bin/aws'
    }
  }
  slurm {
    process {
      executor = 'slurm'
    }
  }
}

//PUBLIS RESULTS
params.publishmode = "copy"
includeConfig 'conf/publish.config'

//GENERATE REPORT https://www.nextflow.io/docs/latest/tracing.html//trace-report
report {
    enabled = true
    file = "${params.infodir}/report.html"
}

//GENERATE TIMELINE https://www.nextflow.io/docs/latest/tracing.html//timeline-report
timeline {
    enabled = true
    timeline.file = "${params.infodir}/timeline.html"
}

//GENERATE PIPELINE TRACE https://www.nextflow.io/docs/latest/tracing.html//trace-report
trace {
    enabled = true
    file = "${params.infodir}/trace.txt"
}

//GENERATE GRAPH REPRESENTATION OF THE PIPELINE FLOW
dag {
    enabled = true
    file = "${params.infodir}/flowchart.dot"
    // file = "${params.infodir}/flowchart.png" //requires graphviz for rendering
}