Hi, I have an RShiny app that has a data processing module which takes some BAM files and performs variant calling. However, currently it does not provide the user a clear idea about the processing stage from the app UI, and the user needs to look at the log files generated. I was thinking of migrating the existing bash scripts to run using Nextflow. Are there any good examples i could look at?

Sure, #CGFUX04HZ is our main variant calling pipeline: https://nf-co.re/sarek