Porting an Existing Pipeline into NextFlow

The client wanted to port an existing pipeline to NextFlow within a short time frame. They were also interested in being able to address any bugs that arose from working with a “new” dataset, modifying or debugging any existing scripts and docker containers and being able to optimize or improve the performance of the pipeline if time allowed.

Delivery

Arrayo got the environment package from the client, including the NextFlow environment. We ported over the “Data Preprocess” pipeline to help solve issues related to data file handling. Arrayo also got up to speed with the “Alignment”, “Variant Calling”, and “Reactivity” pipelines, along with an alpha release for the mechanics and data preprocessing pipelines. We did first hold a beta release of a prototype of all 4 pipelines incorporated. Arrayo then delivered a MVP level Nextflow pipeline. We then tested the pipeline to ensure it worked as intended, as well as providing testing frameworks to ensure that the pipeline would continue to run efficiently.

Value

Arrayo provided a one-to-one port of the client’s Data Pipeline into a workable version of the NextFlow pipeline in a short timeframe, with an additional budget to address fine-tuning and testing frameworks of the pipeline.