default.config

import nextflow.util.SysHelper
import nextflow.Nextflow

// Default inputs/parameters of the pipeline

params {
    min_cpus = 1
    min_memory = 1.MB

    gatk_command_mem_diff = 0.GB
    max_cpus   = SysHelper.getAvailCpus()
    max_memory = SysHelper.getAvailMemory()

    ucla_cds = true

    cache_intermediate_pipeline_steps = false

    metapipeline_delete_input_bams = false
    metapipeline_states_to_delete = ['normal', 'tumor']

    docker_container_registry = "ghcr.io/uclahs-cds"

    gatk_version = "4.2.4.1"
    pipeval_version = "4.0.0-rc.2"
    gatk3_version = "GATK-3.7.0"
    picard_version = "2.26.10"
    samtools_version = "1.17"
    docker_image_gatk = "broadinstitute/gatk:${params.gatk_version}"
    docker_image_pipeval = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
    docker_image_gatk3 = "${-> params.docker_container_registry}/call-gsnp:${params.gatk3_version}"
    docker_image_picard = "${-> params.docker_container_registry}/picard:${params.picard_version}"
    docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"

    gatk_ir_compression = 1

    // These parameters are inferred from the input files. The user can override them in the config file if required.
    reference_fasta_fai = "${-> params.reference_fasta}.fai"
    reference_fasta_dict = "${-> Nextflow.file(params.reference_fasta).resolveSibling(Nextflow.file(params.reference_fasta).getBaseName() + '.dict')}"
    bundle_known_indels_vcf_gz_tbi = "${-> params.bundle_known_indels_vcf_gz}.tbi"
    bundle_contest_hapmap_3p3_vcf_gz_tbi = "${-> params.bundle_contest_hapmap_3p3_vcf_gz}.tbi"
    bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi = "${-> params.bundle_mills_and_1000g_gold_standard_indels_vcf_gz}.tbi"
    bundle_v0_dbsnp138_vcf_gz_tbi = "${-> params.bundle_v0_dbsnp138_vcf_gz}.tbi"
}

// Process specific scope
process {
    // Process results are stored to local cache.
    // If pipeline is launched with the 'resume' option, existing cache results will be used when available
    // rather than re-executing processes
    cache = true

    // Forward process 'stdout' to shell terminal and, consequently, the log file
    executor = 'local'
    
    // Other directives or options that should apply for every process

    // total amount of resources avaible to the pipeline
    cpus = params.max_cpus
    memory = params.max_memory
}

// Enable Docker and configure docker-related options like user and group IDs
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}"
}