Adds more filtering steps to (pre)gwas_filtering

lifebit-ai / gwas

GWAS pipeline using SAIGE

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Adds more filtering steps to (pre)gwas_filtering #8

Closed Vlad-Dembrovskyi closed 4 years ago

Vlad-Dembrovskyi commented 4 years ago

Closes issue #1 Closes issue #15

Adds two additional plink commands described by Thanos in branch kousathanas-support-files. Implements custom file inclusion for plink --keep argument. Updates Dockerfile to include plink(1) for the added commands.

Additionaly: changes --keep to --plink_keep_pheno

Vlad-Dembrovskyi commented 4 years ago

Found an issue when running on CloudOS. Will fix it soon. https://github.com/lifebit-ai/gel-gwas/blob/2c5185dfbc99df79f00e852987a8a67704de174d/nextflow.config#L11

Vlad-Dembrovskyi commented 4 years ago

Fixed the nodata file path. The branch is successfully tested on GEL CloudOS.

Vlad-Dembrovskyi commented 4 years ago

The branch was merged independently by @cgpu to main branch. This can be closed.