Can I use Biopython to automate the NGS pipeline. If yes, which Biopython library can be used to run GATK, SAMTOOLS, bwa, PICARD. ? I hope my question is clear.
For automated pipelines, people use what is known as snakemake
Creating workflows with snakemake and conda
Although, I frequently use shell scripting
While browsing, I also came across Ruffus. How about Ruffus? Which one would be better sankemake or Ruffus? Although, both are python library but there must be some difference
I'd suggest snakemake. As far as I know it's more widely used.
Other options you could explore are NextFlow/FlowCraft