---

#Workflows to convert sra to fastq and run nf-core sarek workflow

name: NFCorePopular
schemaVersion: 1
workflows:
  fetchngs:
    type:
      language: nextflow
      version: 1.0
    sourceURL: workflows/fetchngs
  sarek:
    type:
      language: nextflow
      version: 1.0
    sourceURL: workflows/sarek
data:
#  - location: s3://1000genomes
# - location: s3://seq2-data
#  readOnly: true
#  - location: s3://ngi-igenomes
#  readOnly: true
  - location: s3://roda3
contexts:
  bigMemCtx:
    instanceTypes:                     # Standard types plus r5.8xlarge due to memory requirements of some workflows like sarek
      - "c5.large"
      - "c5.xlarge"
      - "c5.2xlarge"
      - "c5.4xlarge"
      - "c5n.large"
      - "c5n.xlarge"
      - "c5n.2xlarge"
      - "c5n.4xlarge"
      - "m5.large"
      - "m5.xlarge"
      - "m5.2xlarge"
      - "m5.4xlarge"
      - "m5n.large"
      - "m5n.xlarge"
      - "m5n.2xlarge"
      - "m5n.4xlarge"
      - "r5.large"
      - "r5.xlarge"
      - "r5.2xlarge"
      - "r5.4xlarge"
      - "r5.8xlarge"
      - "r5n.large"
      - "r5n.xlarge"
      - "r5n.2xlarge"
      - "r5n.4xlarge"
      - "r5n.8xlarge"
    engines:
      - type: nextflow
        engine: nextflow
  bigMemCtxSpot:
    requestSpotInstances: true
    instanceTypes:             
      - "c5.large"
      - "c5.xlarge"
      - "c5.2xlarge"
      - "c5.4xlarge"
      - "c5n.large"
      - "c5n.xlarge"
      - "c5n.2xlarge"
      - "c5n.4xlarge"
      - "m5.large"
      - "m5.xlarge"
      - "m5.2xlarge"
      - "m5.4xlarge"
      - "m5n.large"
      - "m5n.xlarge"
      - "m5n.2xlarge"
      - "m5n.4xlarge"
      - "r5.large"
      - "r5.xlarge"
      - "r5.2xlarge"
      - "r5.4xlarge"
      - "r5.8xlarge"
      - "r5n.large"
      - "r5n.xlarge"
      - "r5n.2xlarge"
      - "r5n.4xlarge"
      - "r5n.8xlarge"
    engines:
      - type: nextflow
        engine: nextflow