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best tool for the pipeline wrapper

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

pipeline
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updated by Istvan Albert Istvan Albert • written by Sara Sara

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.

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written by Jeremy Leipzig Jeremy Leipzig

2 answers

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.

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written by Ram Ram

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

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written by Istvan Albert Istvan Albert

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