Adds Genetic correlation and heritability analysis within the pipeline

[mcamarad]

Summary:

Adds the option of running heritability with the GWAS summary statistics as well as computing the genetic correlation between your trait of interest and a second trait with GWAS summary statistics imported by the user.

Refactors report to be able to include results from this analysis.

Tasks:

• (1) Make it compatible with SAIGE GWAS output
  • [x] Check which stats are needed.
  • [x] Check that format of columns is compatible
  • [x] Write script to reformat file
• (2 - I) Build processes for heritability
  • [x] Create process to munge statistics to the required format for LDSC.
  • [x] Test the process and see how well it connects
• (2 - II) Build processes for genetic correlation
  • [x] Add external GWAS summary as input.
  • [x] Create process to munge statistics to the required format for LDSC.
  • [x] Test the process and see how well it connects
• (3) Modify report to include LDSC analysis when selected
  • [x] Dump content of log file into the report as no tables are produced
• (4) Add necessary nextflow processes
  • [x] Create switch for turning the analysis on and off
  • [x] Bifurcate report into two process depending on scenarios
• (6) Update nextflow.config and Dockerfile
• (7) Test on CloudOS

Comments:

1. Results in tests might look weird because I used the same test data with different traits. Might need to find a better dataset suited for this.

Test in Lifebit CloudOS

https://cloudos.lifebit.ai/app/jobs/5f8d6aac8f817101130e3607

[mcamarad]

As agreed, integration to report from LDSC output was changed and now it points the user towards looking the actual document generated by the LDSC package. In future iterations we will explore how to integrate and beautify the report so we can fit in in the document.

Ready for round 2 @cgpu !! 🚀 🙏

[mcamarad]

Thanks @cgpu for the really nice feedback! 😃 I added the changes and they should be being tested right now in CloudOS: https://cloudos.lifebit.ai/app/jobs/5f8fd8a68f8171011311b209

[mcamarad]

Thanks a lot for the great feedback and suggestions @cgpu ! :tada: Looking forward to implementing those future improvements! 🚀