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README_WORKFLOW.md

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Workflow Sequest

What happens when you run the workflow?

  1. User uploads (or updates) input_metadata.json file in the fastq/region folder in the input bucket
  2. An S3EventSource watching for that files triggers the fastqLambda to run_workflow and save_metadata to the output bucket.
  3. When run, FASTQ generates the output file bqsr_report/*.hg38.recal_data.csv
  4. This acts as a sentinel file to trigger the packager lambda, which creates a package in the output bucket from everything in the parent of bqsr_report.

Open Issues

  • Why can't we just use the omics events to trigger the packager?
  • S3 notifications for the output bucket are not working. The package is created, but we don't see it the Packages view.