NOTE: project decomissioned and the git repository is no longer public, for more information feel free to reach out to Gervaise Henry

Creating ability to track the running of the Bioinformatics Core Facility’s open source Nextflow pipeline regardless of run environment.The tool utilizes the uses of a custom built REST-API methods with AWS API Gateway which writes to a AWS DynamoDB non-SQL database. A front-end website was built using the static site generator Hugo, though it utilizes custom htmp, css, js code. Continuous integration/continuous deployment is used to automatically build/test/deploy to a AWS S3 bucket, where it is serverlessly hosted. The site queries the database with though the REST-API.

Role:

• Engineer
  • Created the Phase 1 proof of concept independently
  • Architect the methods for further development by additional engineering team

Phase 1 (complete):

• Build API and database to track pipeline runs
• Engineer method for submitting “started” status to the database by Nextflow pipelines regardless of run environment
• Build front-end website which displays run information of several pipelines
• Create CI based build/test/deploy of website

Phase 2 (in process):

• Develop methods for Nextflow deploying status updates
• Integrate into all BICF pipelines (see BICF Pipelining project)