version 1.0

import "../../../../tasks/wdl/ImputationTasks.wdl" as tasks

workflow QuotaConsumed {
    # if this changes, update the quota_consumed_version value in Glimpse2LowPassImputation.wdl
    String pipeline_version = "0.0.2"

    input {
        # service expects only cram_manifest even though main wdl can alternatively take input arrays
        File cram_manifest
        String output_basename

        Array[String] contigs
        # this is the path to a directory that contains sites vcf, sites table, and reference chunks file. should end with a "/"
        String reference_panel_prefix
        File fasta
        File fasta_index
        File ref_dict
    }

    call CountCramsFromManifest {
        input:
            cram_manifest = cram_manifest
    }

    output {
        Int quota_consumed = CountCramsFromManifest.cram_manifest_count
    }
}

task CountCramsFromManifest {
    input {
        File cram_manifest

        String docker = "us.gcr.io/broad-dsde-methods/ubuntu:20.04"
        Int cpu = 1
        Int memory_mb = 4000
        Int disk_size_gb = ceil(size(cram_manifest, "GiB")) + 10
    }

    command <<<
        set -e -o pipefail

        grep ".cram" ~{cram_manifest} | wc -l > cram_manifest_count.txt
    >>>

    output {
        Int cram_manifest_count = read_int("cram_manifest_count.txt")
    }
    runtime {
        docker: docker
        disks: "local-disk ${disk_size_gb} HDD"
        memory: "${memory_mb} MiB"
        cpu: cpu
        preemptible: 0
        maxRetries: 1
        noAddress: true
    }
}