best tool for the pipeline wrapper

Question

[Sara]

I have made a pipeline for our scRNAseq and every time I have to copy the workflow to the directory and run it. So I decided to make a wrapper for it to just give the input data location and run the pipeline. Do you know which program or programming language is the best for this purpose

[Jeremy Leipzig]

Actually I think it's good you have to copy the workflow to the directory to run it. Then at least you have a versioned paper trail.

Answer 1

[Ram]

Go for snakemake. It can wrap a shell command with minimum work, can be incrementally abstracted and customized and personally, I love the --dry-run option.

Answer 2

[Istvan Albert]

Here it depends on how complicated your pipeline is,

start with shell scripts, you can use a makefile,

as you progress start exploring more advanced solutions like snakemake that Ram suggested