This PR does the following:

Removes gwas_filtering_bin and gwas_filtering_qual as they overlap heavily - instead, new processes vcf2plink, filter_missingness and calculate_hwe are introduced which isolate by logic the QC steps previously contained in gwas_filtering_x steps
Previously, missingness check and filter was not run for quantitative traits. This is now implemented.
Combine separate gwas_1_fit_null_glmm processes with correct trait type and inverse normalization handling for quantitative trait type
Updates CI tests to use --config
Implements support for specifying covariate columns as input for the first step of SAIGE (model fitting)
Implements support for single VCF as input for second step of SAIGE

Test

To reproduce locally:

git clone https://github.com/lifebit-ai/gel-gwas.git
git checkout refactoring_fixes
wget -qO- https://get.nextflow.io | bash
NXF_VER=20.01.0 ./nextflow run main.nf --config conf/test_binary.config
NXF_VER=20.01.0 ./nextflow run main.nf --config conf/test_qt

GEL production

Lifebit CloudOS job link

lifebit-ai / gwas

Refactoring fixes #105

This PR does the following:

Test