I just started a job as the first bioinformatics scientist in a large pharmaceutical company. I am new to pharma and human genomics (previously did microbial bioinformatics), and I am trying to get a workstation and computing environment ordered, up and running. I requested a souped-up Linux desktop for scripting work and pipeline development, and plan to outsource bigger jobs to AWS or something similar. However, my request for a Linux-OS was denied because the company is Windows-exclusive. The IT department offered me Biovia Pipeline Pilot NGS as a Windows-based alternative to the many Linux-based open source tools.
Is anyone here familiar or have experience with this software? How customizable and adaptable is it to new NGS tools that are being developed? It's obviously very expensive and I'd prefer not to go there, but I'd like to better understand its capabilities and limitations, so that I can re-submit a stronger justification for the open source tools if it's not suitable. Any comments or suggestions would be appreciated.