Happy new year everyone 🙂 I would like to improve my processing pipelines (aligning, variant calling etc). Currently they are written in bash. I find that certain things are much easier in other languages (R, python, perl) than bash. Python may allow robust error detection as well.
Do people still use 100% bash or mixture of bash and other languages, performing system calls when required? How are these integrated in CWL/Snakemake etc? Thanks for sharing your insights!