Pipelines in bash vs other languages

Question

[jaynishshah]

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!

[jaynishshah]

Thanks Pierre. gotta learn more bash then ;)

Answer 1

[Pierre Lindenbaum]

you write bash commands in Makefile, Snakemake, Nextflow , etc... . The workflow manager is 'only' here to schedule/parallelize/submit/not-redo-existing things