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How to configure workflows when using in another workflow. #3

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SilasK opened this issue Jan 27, 2023 · 0 comments

SilasK commented Jan 27, 2023

Hey, I start using snakmake workflows and modules.

My goal is to factorize a large snakemake pipeline in smaller modules that then might be recombined in new piplines.

I saw that sometimes you require many config variables e.g., in the dna-seq-short-read-circle-map or even more in the dna-seq-gatk-variant-calling

How exactly should one ensure that all the config variables are correctly defined when the module will be used in a new pipeline?

E.g. the template config is empty.

Is there a way to ensure updates to the config are also available in new pipelines?

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