misc. improvements

[espenhgn]

• [ ] link to paper/mention COSGAP across main repos.
• [ ] improve usecase using UKB datas
• [x] Add proper citations to original research papers in table with tool overview (fix in documentation)
• [ ] Improve usecases/tutorials (QC, PCA, phasing, imputation, etc. missing in tutorials).
• [x] Autodoc gwas.py and pgs_toolkit codes for online docs
• [x] conda environment for easier setup of project dependencies (git-lfs, singularity, ...) on e.g., HUNT Cloud

[ofrei]

• [ ] gwas.py, LDpred2 and pgs_toolkid currently lack documentation in docs folder; instead they are documented within scripts folder, often by pointers to usecases. Good to discuss how this documentation can be consolidated.
• [ ] similarly, reference data is mostly documented in README files spread across the reference folder.
• [ ] refine documentation by moving away project-specific instructions (e.g. private COMORMENT reference repo, TSD locations, MoBa examples, etc)
• [ ] do we expect users to use README files on github, or sphinx online docs https://comorment-containers.readthedocs.io/en/latest/index.html ? I suggest later. If that's the case we need to improve the structure of the Table of Content / navigation panel
• [ ] Let's discuss how best to represent LDpred2 command-line interface scripts in this repository; is this a separate software package, or part of our GWAS / PGS pipelines? If later, how this connects to geno/pheno/sumstats format specifications?

[ofrei]

• [x] opensnp is imputed; improve pheno.csv file with extra simulated phenotypes
• [ ] opensnp datas in both PLINK1, PLINK2, VCF, BGEN formats
• [ ] use opensnp in all tutorials (gwas & pgs)
• [ ] use ukb in larger demos
• [x] use sphinx for documentation
• [x] split out "internal use" and "dev instructions" from user documentation
• [ ] impose more structure in the docs
• [ ] gwas.py pgs & pgs_toolkit.
• [ ] docstrings for gwas.py and/or --help output
• [ ] include info / documentation on software from othe containers (magma.sif, HDL.sif, etc)

[espenhgn]

For putting the documentation at https://cosgap.readthedocs.io I need to disable the old build and set it up anew. It wasn't enough to rename the project on readthedocs.io. However, it would be good then to keep the old versioned project documentation history in the old location I think.

Edit: https://cosgap.readthedocs.io/en/latest/index.html is now alive. Kept the old one for now.

[github-actions[bot]]

This issue appears to be stale due to non-activity