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zrcjessica / demux

A Snakemake pipeline for running single-cell demultiplexing simulations.
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a snakemake pipeline #4

Closed aryarm closed 4 years ago

aryarm commented 4 years ago

It'd be great if we could execute this workflow as a Snakemake pipeline, so that we can run it multiple times for different inputs. And parallelize steps. And organize things.

zrcjessica commented 4 years ago

We may want to run this entire simulation with different doublet rates (currently I have it set at 30%). As a result, we probably need to modify our scripts such that the output file names or directory names include the doublet rate used for the simulation.

aryarm commented 4 years ago

good point ok, I'll include that in the pipeline

zrcjessica commented 4 years ago

Is it better to include this information in the file names or the directory names?