default.config

import nextflow.util.SysHelper

docker {
    enabled = true
    // Pass user's UID/GID and group IDs to Docker
    uid_and_gid = "-u \$(id -u):\$(id -g)"
    all_group_ids = "\$(for i in `id --real --groups`; do echo -n \"--group-add=\$i \"; done)"

    runOptions = "${uid_and_gid} ${all_group_ids}"
    }

params {
    max_cpus   = SysHelper.getAvailCpus()
    max_memory = SysHelper.getAvailMemory()

    cache_intermediate_pipeline_steps = false
    save_intermediate_files = true

    ucla_cds = true

    blcds_registered_dataset = false

    // Pipeline tool versions
    delly_version = '0.9.1'
    bcftools_version = '1.12'
    validate_version = '2.1.5'

    // Docker tool versions
    docker_image_delly = "blcdsdockerregistry/delly:${params.delly_version}"
    docker_image_bcftools = "blcdsdockerregistry/bcftools:${params.bcftools_version}"
    docker_image_validate = "blcdsdockerregistry/validate:${params.validate_version}"
    }

process {
    executor = 'local'
    echo = true
    cache = true
    }