nextflow.config

/*
================================================================
  Set default parameters
================================================================

Any parameters provided by the user with a -params-file or
with -- command-line arguments will override the values
defined below.
*/
params {
    help               = false
    input_folder       = false
    output_folder      = "${launchDir}/results/"
    chrom_mapping_file = "http://gitlab.cbra.com/dlopez/csvs_prs/raw/master/resources/rename-chrs.txt"
    capture_bed        = "http://gitlab.cbra.com/dlopez/csvs_prs/raw/master/resources/intersect_common.bed"
    exome              = false
    shapeit4_map_files = false
    minimac4_ref_files = false
    reference_genome   = false

    // Set the containers to use for each component
    container__bcftools = "quay.io/biocontainers/bcftools:1.16--hfe4b78e_1"
    container__plink    = "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
    container__shapeit4 = "quay.io/biocontainers/shapeit4:4.2.2--h24bf969_1"
    container__minimac4 = "rtibiocloud/minimac4:1.0.1"
}


/*
================================================================
  set profiles
================================================================
Set cpus/memory or create your own profile according
to your HPC
*/
profiles {
  singularity {
    singularity.autoMounts = true
    singularity.enabled = true
  }

  docker {
    docker.enabled = true
    docker.fixOwnership = true
  }

  slurm {
    process {
      executor = 'slurm'
      cpus = 1
      memory = '4 GB'
      time = '12h'
      beforeScript = 'ml singularity'

      withLabel: 'parallel' {
        cpus = 8
        memory = 32.GB
      }
    }
  }

  debug { 
    process.beforeScript = 'echo $HOSTNAME' 
  }

  test {
    params {
      input_folder       = "${projectDir}/test/"  
      chrom_mapping_file = "http://gitlab.cbra.com/dlopez/csvs_prs/raw/master/resources/rename-chrs.txt"
      capture_bed        = "http://gitlab.cbra.com/dlopez/csvs_prs/raw/master/resources/intersect_common.bed"
      reference_genome   = "${projectDir}/resources/ref/hs37d5.fa"
      exome              = true
      shapeit4_map_files = "${projectDir}/resources/shapeit4/chr*.b37.gmap.gz"   
      minimac4_ref_files = "${projectDir}/resources/minimac4/*.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz"
    }
  }
}

manifest {
        name = 'PRS_pipeline'
        author = 'Daniel López López'
        homePage = 'http://gitlab.cbra.com/dlopez/csvs_prs.git'
        mainScript = 'main.nf'
        nextflowVersion = '>=22.10.6'
        version = '1.0.0'
}


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


dag {
  enabled = true
  file = "${params.output_folder}/report/pipeline_dag.svg"
  overwrite = true
}
report {
  enabled = true
  file = "${params.output_folder}/report/execution_report.html"
  overwrite = true
}
timeline {
  enabled = true
  file = "${params.output_folder}/report/execution_timeline.html"
  overwrite = true
}
trace {
  enabled = true
  file = "${params.output_folder}/report/execution_trace.txt"
  overwrite = true
}