allenday

name: sra_download
description: use Google Pipeline API to download an SRA run, reformat it as unaligned BAM, and upload it to Google Cloud Storage.  Run it like this: gcloud alpha genomics pipelines run --inputs SAMPLE=XXXXX --inputs RUN=XXXXX --outputs OUTPUT_FILE=gs://XXXXX --pipeline-file=sra_download.yaml
resources:
  #increase boot disk from 10GB to 50GB to accomodate intermediate files
  bootDiskSizeGb: 50
  #specify multiple zones so this pipeline will run in parallel
  zones:
  - us-west1-a
  - us-west1-b
  - us-east1-b