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Showing posts with the label Snakemake
Snakemake - Dynamically Derive The Targets From Input Files

Snakemake - Dynamically Derive The Targets From Input Files

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I have a large number of input files organized like this: data/ ├── set1/ │ ├── file1_R1.fq.gz │ … Read more Snakemake - Dynamically Derive The Targets From Input Files
How To Use Expand In Snakemake When Some Particular Combinations Of Wildcards Are Not Desired?

How To Use Expand In Snakemake When Some Particular Combinations Of Wildcards Are Not Desired?

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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?
Parallelizing Snakemake Rule

Parallelizing Snakemake Rule

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Sorry if this is a naive question, but I'm still trying to wrap my head around the intricacies … Read more Parallelizing Snakemake Rule
Using Conda Enviroment In Snakemake On Sge Cluster Problem

Using Conda Enviroment In Snakemake On Sge Cluster Problem

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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
Specifying Python Version Within Snakemake Using Script Parameter

Specifying Python Version Within Snakemake Using Script Parameter

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I have some code that I am incorporating into a Snakemake pipeline. I also want to be able to run t… Read more Specifying Python Version Within Snakemake Using Script Parameter