mcamarad
commented
4 years ago Update
This PR now also solves: #39, #40 & #10537
Changelog
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Docs with examples and parameter description added here.
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Refactor nextflow pipeline with more consistent and descriptive parameters (snakecased)
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Adds support to continuous variables as PHE
- [x] Creates switch around trait_type nextflow parameter.
- [x] Adds
traitType&invNormalizeto SAIGE GWAS processes - [x] Removes missingness filtering step for quantitative trait GWAS to avoid pipeline errors
- [x] Refactor report to allow outputs from quantitative trait GWAS
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Adds transformation of continuous variables
- [x] zscores, log, log2 and none
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Add fixes to support
pheno_colwith parentheses across the pipeline- [x] Solves issues in which filenames with parentheses in their names break the pipeline in AWS
Tests on CloudOS
Binary
https://cloudos.lifebit.ai/app/jobs/5f7dda448f8171011301cb89
Quantitative
https://cloudos.lifebit.ai/app/jobs/5f7dda318f8171011301cb69
Comments
@cgpu ready for review! :tada:
Summary
Working on Internal CloudOS: https://cloudos.lifebit.ai/app/jobs/5f75fd8eff510d01135c5388
Integrates CB output with GWAS pipeline, adds multiple design matrix construction, transformation layer for encoding of variables and connects phenotypic data with the rest of the pipeline.