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lifebit-ai / gwas

GWAS pipeline using SAIGE
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Hardcoded sampleFile name in step2_SPAtests.R #88

Closed cgpu closed 3 years ago

cgpu commented 3 years ago

https://github.com/lifebit-ai/gel-gwas/blob/2664c72dcbfb2a63c5d23ccd726d27c1f490d2ef/main.nf#L539

mcamarad commented 3 years ago

Thanks for pointing this @cgpu !!

This variable refers to: "Path to the file that contains one column for IDs of samples in the dosage file. For version >= 0.38, this file is only needed for bgen files". -> We use v. 0.39 of SAIGE

I will parametrize it, but as we don't use bgen files it won't be an issue or provoke one for now.

evagradovich commented 3 years ago

Resolved in https://github.com/lifebit-ai/gel-gwas/pull/105