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I am trying to index a reference genome on a pipeline with snakemake and I made this rule: rule ref… Read more Star Index Issues To The Step 4

Related: SnakeMake rule with Python script, conda and cluster I have been trying to set up my Snake… Read more Using Conda Enviroment In Snakemake On Sge Cluster Problem

I'm trying to first generate 4 files, for the LETTERS x NUMS combinations, then summarize over … Read more How To Do A Partial Expand In Snakemake?

Snakemake appears to traverse the DAG in a breadth-first manner. Is it possible (e.g. through an op… Read more Snakemake: Tranverse Dag Depth-first?

Let's suppose that I have the following files, on which I want to apply some processing automat… Read more How To Use Expand In Snakemake When Some Particular Combinations Of Wildcards Are Not Desired?

Perhaps this question has already been answered but I could not come up with the correct query to f… Read more Snakemake Workflow On Split Files

Is it possible to pass custom command line arguments to snakemake scripts? I have tried, but execut… Read more Use Of Argparse In Snakemake Script