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snakemake-workflows / dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow
MIT License
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use peppy #22

Closed stolarczyk closed 3 years ago

stolarczyk commented 4 years ago

@vreuter, @nsheff, @johanneskoester

This is a reiteration of #8, but with a re-written version of peppy that supports the config format revamp discussed in https://github.com/pepkit/peppy/issues/334

nsheff commented 4 years ago

@stolarczyk can you update this to the now-almost-final peppy updates when you get a chance?

nsheff commented 4 years ago

Hi @johanneskoester can you take a look at this when you get a moment?

nsheff commented 4 years ago

FYI we released peppy so it's now live with all the updates we discussed.

johanneskoester commented 4 years ago

Hi Nathan, yes, I'll have a look. Still not a fan of the snake_config tag, but maybe it can be used in a different way. I just cannot promise that I will be able to evaluate it immediately.

Best, Johanne

nsheff commented 4 years ago

Still not a fan of the snake_config tag

that's not build in to peppy -- it's just used here. you could instead just put all options in config.yaml directly into the PEP... is that what you're wanting?

johanneskoester commented 4 years ago

Thanks for the clarification! I will probably keep the PEP and the pipeline config separate then. My idea is that the PEP should just describe the samples, while the pipeline describes the analysis. This way, one can easily plug the very same PEP into a completely different pipeline (other WMS, other analysis, ...).