I would like to call germline variants with GATK4, i.e. map with bwa mem, mark duplicates ecetera ... I haven't done that in a while but back then it was like a few commands. So now that I'm checking the pipeline commands, what I find is this: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/master/PairedEndSingleSampleWf.wdl I'm not even sure whether this is the right file to look at? And I do not even know what a ".wdl" file is nor am I interested in learning yet another language. Why do I see 1500 lines of code, I was expecting just a few steps / GATK subcommand calls? Like HaplotypeCaller, filter ... ecetera ... what happened to those kind of tutorials?