params {
    vcf             = null
    job_id          = null        // omit for a dry run that parses but does not load
    outdir          = "results"
    assembly        = "GRCh38"
    vep_cache       = "${projectDir}/cache/vep"   // INSTALL.pl -a cf -s homo_sapiens -y GRCh38 -c <dir>
    vep_plugin_data = null        // CADD + AlphaMissense modules and data; plugins skipped when null
    cadd_snv        = "whole_genome_SNVs.tsv.gz"
    cadd_indels     = "gnomad.genomes.r4.0.indel.tsv.gz"
    alphamissense   = "AlphaMissense_hg38.tsv.gz"
    // The driver image sets this to the loader image built from the same commit.
    loader_image    = System.getenv('RARELENS_LOADER_IMAGE') ?: 'rarelens/loader:dev'

    // gcp profile; the Argo workflow provides these through the pipeline-config ConfigMap.
    project         = System.getenv('GCP_PROJECT')
    region          = System.getenv('GCP_REGION') ?: 'europe-west2'
    bucket          = System.getenv('GCS_BUCKET')
}

process {
    shell = ['/bin/bash', '-euo', 'pipefail']
    withName: VEP        { container = 'ensemblorg/ensembl-vep:release_113.0'; cpus = 4; memory = '8 GB' }
    withName: NORMALISE  { container = 'quay.io/biocontainers/bcftools:1.20--h8b25389_0' }
    withName: LOAD_DB    { container = params.loader_image }
}

profiles {
    docker {
        docker.enabled      = true
        docker.envWhitelist = ['DATABASE_URL']
        // Lets the loader reach a Postgres published on the host (docker-compose's port 5432).
        docker.runOptions   = '--add-host=host.docker.internal:host-gateway'
    }
    gcp {
        // The driver runs in the Argo pod; each task runs as a Google Batch job, which is what a
        // gs:// work directory requires (the k8s executor needs a shared ReadWriteMany volume).
        workDir = "gs://${params.bucket}/work"
        params.vep_cache = "gs://${params.bucket}/refs/vep"
        google {
            project  = params.project
            location = params.region
            batch.serviceAccountEmail = "rarelens-pipeline@${params.project}.iam.gserviceaccount.com"
            batch.network    = "projects/${params.project}/global/networks/rarelens-vpc"
            batch.subnetwork = "projects/${params.project}/regions/${params.region}/subnetworks/rarelens-gke"
        }
        process {
            executor = 'google-batch'
            // Google Secret Manager secret created by Terraform (infra/terraform/secrets.tf).
            withName: LOAD_DB { secret = 'DATABASE_URL' }
        }
    }
}