nextflow.config_lsf_template

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

params {
    pgs_num_from = <PGS ID start number, e.g. '20' for PGS000020>
    pgs_num_to = <PGS ID end number, e.g. '140' for PGS000140>
    genomebuild = <target genomebuild, e.g. '38'>
    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>
    vars_list_file_path = <path to the variants list file name, e.g. "$root_dir/vars_list.txt">
    var_files_path = <wildcard file name to store the variant coordinates on each VCF file (i.e. chromosome), e.g. "$root_dir/vars_files/vars_chr*.txt">
    merged_var_file_path = <file to merge the content of all the var_files_path, e.g. "$root_dir/vars_files/merged_var_file.txt">
    no_coord_var_file_path = <path to the file listing the variants missing in the VCF files that will be searched via the Ensembl REST API, e.g. "$root_dir/vars_files/no_coord_var_file.txt">
    missing_var_file_path = <path to the file listing the variants missing in the VCF files and the Ensembl REST API, e.g. "$root_dir/vars_files/vars_with_missing_info.txt">
    var_file_path_ensembl = <path to the file containing all the variant data fetched via the Ensembl REST API, e.g. "$root_dir/vars_list_ensembl.txt">
    sqlite_file_path = <path to the SQLite database>
    loc_pipeline = <path to the 'scoring_files_pipeline' directory>
    loc_score_dir = <path to the directory where the scoring files are stored, e.g. '${params.work_dir}/scorefiles/'>
    loc_vcftools = <path to the vcftools bin file, e.g. "..../bin/vcftools">
    loc_vcfs = <path to the 'Ensembl VCF' directory>
    loc_filtered_vcfs = <path to the directory to store the filtered VCF files>
    loc_variants_files = <path to the directory to store the var_files, e.g. "$root_dir/vars_files">
    vcf_file_prefix = <file name prefix used on each VCF files, e.g. "homo_sapiens-chr">'
}

process {
    queue = 'production-rh74'
    executor = 'lsf'
    withLabel: medium_mem {
        memory = '4 GB'
    }
    withLabel: retry_increasing_mem {
        errorStrategy = 'retry'
        memory = {1.GB * task.attempt}
        maxRetries = { task.exitStatus in [130,140] ? 6 : 2 }
    }
}