Bioinformatics - Scalable NGS microbiome pipeline
A wet-lab Microbiome Lab of a Switzerland research institute requested help with bioinformatic processing of their NGS data. They had a general idea of what steps they needed to perform and even created a preliminary bash script. But that script was 4000 lines long, hard to grasp and running for a week on their local computers.
That is where Offsiteteam stepped in.
NextFlow pipeline programming
Cloud AWS Batch execution
Isolated Docker environments
Terraform for Infrastructure as a Service
Refactor a messy R/Bash/Python pipeline script written by a PhD student into reusable and easy to understand pipeline, allowing multiple runs.
A parallel-ready NextFlow pipeline was created, accompanied by Terraform script to create an AWS infrastructure allowing to run this pipeline in a cloud.
Now the script can be run in a HPC cloud, allowing multiple experiments and easily understood by any member of a lab.