nextflow_list.config_lsf_template

root_dir = <path to the working directory (other than Nextflow's)>

params {
    pgs = <list of PGS IDs to harmonize, e.g. ['PGS000020','PGS000140']>
    pgs_ids_file = <name of the locally generated PGS IDs list file, e.g. "pgs_ids.txt">
    rest_api_url = <URL to the REST API server>
    loc_scripts = <path to the pgs-harmonizer directory, e.g. /Users/my_account/pgs-harmonizer/ (absolute) or ../../../ (relative)>
    loc_files = <path to the Scoring files directory>
    loc_hmoutput = <path to the HmPOS output directory, e.g. "$root_dir/HmPOS">
    loc_hmoutput_vcf = <path to the HmVCF output directory, e.g. "$root_dir/HmVCF">
    loc_var2location = <path to the directory containing the variant coordinates Knowledge Bases>
    loc_vcfs = <path to the Ensembl VCFs - optional if they are located in 'map/vcf_ref/'>
    loc_staged = <path to the directory containing the final version of the harmonized files, e.g. "$root_dir/HmFinal">
    hm_version_sqlite_file_path = <path to the Harmonization Knowledge Base, e.g. 'pgs_harmonizated_kb.db'>
}

// Only to be used if the script is running on LSF, on the cloud or in a container.
// More information is available here: https://www.nextflow.io/docs/latest/executor.html
executor {
  name = 'lsf'
  queueSize = 25
}

process {
  queue = 'short'
  withLabel: medium_mem {
    memory = '1 GB'
  }
  withLabel: retry_increasing_mem {
    errorStrategy = 'retry'
    memory = {2.GB * task.attempt}
    maxRetries = { task.exitStatus in [130,140] ? 10 : 2 }
  }
  withLabel: retry_increasing_big_mem {
    errorStrategy = 'retry'
    memory = {3.GB * task.attempt}
    maxRetries = { task.exitStatus in [130,140] ? 10 : 2 }
  }
}