nextflow.config

// Global default params, used in configs
params {
    // optional file paths [optional input](https://nextflow-io.github.io/patterns/optional-input/)
    atac_file = "$projectDir/assets/NO_ATAC_FILE"
    broad_fine_mapping = "$projectDir/assets/NO_FILE"  // TODO: simplify, required if ATAC mode 

    // required parameters
    studies = null  // required input: "/path/to/your/studies.tsv"
    tss_file = null  // required input: "/path/to/your/tss_cell_type_exp.txt.gz"
    cell_types = null  // required input: "/path/to/your/tss_cell_type_exp.txt"

    // other default values
    gene_chunk_size = 100
    vcf_files_1000G = "/nfs/cellgeni/pipeline-files/1000G/20190312/European/"  // looking for `chr*.maf0.001.vcf.gz` in this folder
}

// Configuring LSF job submission parameters for each process
executor {
  name = 'lsf'
  perJobMemLimit = true
}

singularity {
  enabled     = true
  autoMounts  = true
  cacheDir = '/nfs/cellgeni/singularity/images/'
  runOptions = '-B /lustre,/nfs --nv'
}

process {
  
  maxRetries = 3
  errorStrategy = {
    switch (task.exitStatus) {
      case 130:  // out of memory
        retries = 3; break
      default:
        return 'terminate'
    }
    return (task.attempt <= retries) ? 'retry' : 'ignore' 
  }
  beforeScript = "echo Queue: \$LSB_QUEUE"

  withName: split_studies {
    cpus = 1
    memory = { 10.MB * task.attempt }
    queue = "small"
    maxForks = 10
  }

  withName: fetch_irods {
    cpus = 4
    memory = { 4.GB * task.attempt }
    queue = "transfer"
    maxForks = 5
  }

  withName: run_LDSC {
    cpus = 1
    errorStrategy = {
      switch (task.exitStatus) {
        case 130:  // out of memory
          retries = 3; break
        case 140:  // runtime limit
          retries = 1; break
        default:
          return 'terminate'
      }
    memory = { 2.GB * task.attempt }
    queue = { task.attempt > 1 && task.exitStatus == 140 ? 'week' : 'normal' }
    maxForks = 1000
    container = '/nfs/cellgeni/singularity/images/fgwas_v0-2.sif' 
  }

  withName: collect_LDSC {
    cpus = 1
    memory = { 5.GB * task.attempt }
    queue = "normal"
    maxForks = 1000
  }

  withName: run_HM {
    cpus = 1
    memory = { 5.GB * task.attempt }
    queue = "normal"
    maxForks = 1000
    container = '/nfs/cellgeni/singularity/images/fgwas_v0-2.sif' 
  }

  withName: plot_forest {
    cpus = 1
    memory = { 250.MB * task.attempt }
    queue = "small"
    maxForks = 1000
    container = '/nfs/cellgeni/singularity/images/fgwas_v0-2.sif' 
  }
}

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

// Capturing Nextflow log files into a reports directory
timeline {
  enabled = true
  overwrite = true
  file = "fgwas-reports/timeline.html"
}

report {
  enabled = true
  overwrite = true
  fields = 'task_id,process,status,queue,exit,status,attempt,duration,realtime'
  file = "fgwas-reports/report.html"
}

trace {
  enabled = true
  overwrite = true
  file = "fgwas-reports/trace.txt"
}