I am currently running a brief variant calling project. I was running GATK using standard tool commands in a Linux shell when I came across a blog on Workflow Description Language (WDL) scripting for GATK which runs on cromwell.
What would be the primary differences in running GATK (4.0.11) using either one of them ? I read that WDL is an "analysis pipieline" but haven't got much of an idea as to what that means in terms of bioinformatics.
Thank you ! Pardon me if the question sounds dumb but what would be the difference vis a vis just piping commands together in a bash shell using the standard tools-specific commands ? What would be the primary advantage of a WDL script / Cromwell engine in that aspect ? Does it streamline my processes more efficiently and work faster ?
I'm essentially looking for a way to streamline and combine as many steps as possible (since I have 100+ paired samples to align and call) in a fast manner.
parallelization, don't re-make existing files on failure, etc...