terraform {
  backend "s3" {
    bucket  = "variant-spark-july"
    key     = "variantspark-k/tfstate"
    region  = "us-west-2"
    profile = "default"
  }
}

provider "aws" {
  profile = "${var.profile}"
  region  = "${var.default_region}"
}

provider "aws" {
  alias   = "use1"
  profile = "${var.profile}"
  region  = "us-east-1"
}

module "eks-vpc" {
  source         = "modules/eks-vpc"
  "cluster-name" = "${var.cluster-name}"
}

module "eks-master-role" {
  source = "modules/eks-master-role"
}

module "eks-master-security-group" {
  source = "modules/eks-master-security-group"
  vpc_id = "${module.eks-vpc.vpc_id}"
}

module "eks-worker-role" {
  source = "modules/eks-worker-role"
}

module "eks-worker-security-group" {
  source = "modules/eks-worker-security-group"

  vpc_id                   = "${module.eks-vpc.vpc_id}"
  master_security_group_id = "${module.eks-master-security-group.security_group_id}"
  "cluster-name"           = "${var.cluster-name}"
}

module "eks" {
  source                   = "modules/eks"
  cluster_name             = "${var.cluster-name}"
  vpc_id                   = "${module.eks-vpc.vpc_id}"
  public_subnets           = "${module.eks-vpc.public_subnets}"
  master_role_arn          = "${module.eks-master-role.master_role_arn}"
  master_security_group_id = "${module.eks-master-security-group.security_group_id}"
  worker_role_arn          = "${module.eks-worker-role.worker_role_arn}"
  worker_profile_name      = "${module.eks-worker-role.worker_profile_name}"
  worker_security_group_id = "${module.eks-worker-security-group.security_group_id}"
  caller_profile           = "${var.profile}"
  eks_key_name             = "${module.kops-ssh.key_name}"
  spark_user_arn           = "${module.kops-user.arn}"
}

module "kops-user" {
  source = "modules/kops-user"
}

module "state-storage" {
  source = "modules/state-storage"
}

module "input-bucket" {
  source = "modules/input-bucket"
}

module "kops-ssh" {
  source = "modules/ssh-key"
}

data "aws_availability_zones" "available" {}

data "template_file" "env" {
  template = "${file("templates/env.tpl")}"

import "https://raw.githubusercontent.com/broadinstitute/viral-pipelines/master/pipes/WDL/tasks/tasks_taxon_filter.wdl" as taxon_filter
import "https://raw.githubusercontent.com/broadinstitute/viral-pipelines/master/pipes/WDL/tasks/tasks_assembly.wdl" as assembly

workflow assemble_denovo_with_deplete {
  
  call taxon_filter.deplete_taxa

  call taxon_filter.filter_to_taxon {
    input:
      reads_unmapped_bam = deplete_taxa.cleaned_bam
  }

  call assembly.assemble {
    input:
      reads_unmapped_bam = filter_to_taxon.taxfilt_bam
  }

  call assembly.scaffold {
    input:
      contigs_fasta = assemble.contigs_fasta,
      reads_bam = filter_to_taxon.taxfilt_bam
  }

  call assembly.refine_2x_and_plot {
    input:
      assembly_fasta = scaffold.scaffold_fasta,
      reads_unmapped_bam = deplete_taxa.cleaned_bam
  }
}