---
name: GATKOnMiniwdl
schemaVersion: 1
workflows:
  gatk4-data-processing:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./gatk4-data-processing
  gatk4-germline-snps-indels:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./gatk4-germline-snps-indels
  gatk4-basic-joint-genotyping:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./gatk4-basic-joint-genotyping
  seq-format-validation:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./seq-format-validation
  bam-to-unmapped-bams:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./seq-format-conversions/bam-to-unmapped-bams
  cram-to-bam:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./seq-format-conversions/cram-to-bam
  interleaved-fastq-to-paired-fastq:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./seq-format-conversions/interleaved-fastq-to-paired-fastq
  paired-fastq-to-unmapped-bam:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./seq-format-conversions/paired-fastq-to-unmapped-bam
  gatk4-rnaseq-germline-snps-indels:
    type:
      language: wdl
      version: 1.0
    sourceURL: ./gatk4-rnaseq-germline-snps-indels
data:
  - location: s3://gatk-test-data
    readOnly: true
  - location: s3://broad-references
    readOnly: true
  - location: s3://1000genomes-dragen-3.7.6
    readOnly: true
  - location: s3://healthai-public-assets-us-east-1/agc-demo-data/*
    readOnly: true
contexts:
  # The on demand context uses on-demand EC2 instances which may be more expensive but will not be interrupted
  onDemandCtx:
    requestSpotInstances: false
    engines:
      - type: wdl
        engine: miniwdl

  # The spot context uses EC2 spot instances which are usually cheaper but may be interrupted
  spotCtx:
    requestSpotInstances: true
    engines:
      - type: wdl
        engine: miniwdl