feat: Introduce GENS to WGS workflow

[mathiasbio]

This PR:

Adds rules and a script to create the final coverage.bed and baf.bed files to upload to GENS.
Only active for WGS samples.

Added new functionality in BALSAMIC to allow visualisation of coverage and BAF in GENS in WGS:

• New command line arguments for config case required for creating GENS files
• Additional DNAscope call using gnomad vcf of > 0.05 AF as --given command for creation of BAF-files
• Rules using GATK rules for creating normalised coverage bed-files
• Python-script for pre-processing of created files into different window-sizes for zoom feature in GENS
• Workflow for generation of GENS PON
• Flexibility in PON workflow creation, choosing wither CNVkit or GENS
• Created 2 PONs for GENS coverage based on 100 female, and male WGS normal samples
  • balsamic_pon_100bp.female.v1.hdf5
  • balsamic_pon_100bp.male.v1.hdf5

New rules seen here:

Changed:

• Added extra arguments for starting PON workflow creation (--pon-workflow)

Pre-steps:

Due to the presence of the decoy sequence hs37d5 in the MIP reference, which is missing from the BALSAMIC reference fasta, which could absorb reads in the creation of the PON in MIP and lead to a small risk of false positive / negative CNVs in GENS from balsamic using this PON, new PONs were created for balsamic (config and project structure here /home/proj/development/cancer/development_files/GENS_PON_CREATION):

• Creation of balsamic GENS PON 100 WGS, 30X from females
• Creation of balsamic GENS PON 100 WGS, 30X from males

Integrity tests:

• Successfully run unitedbeagle T/N TGA without GENS reference-inputs
• Successfully generated final GENS files for WGS T/N case
• GENS files are saved in hk files.

Practical use-case tests:

https://gens-stage.scilifelab.se/

• View CNVs in GENS for fleetjay. Quick overview of normal and tumor GENS results looks good! (2023-10-10 import date)
• View CNVs in GENS for new case with new PONS (trustyfish).
• upload manually to housekeeper: (housekeeper add file -kip -b trustyfish -t bed -t fracsnp -t scout -t gens -t ACC /path/to/file/analysis/cnv/ACC.baf.bed.gz etc...)
• upload manually to GENS (cg upload gens trustyfish)
• view and verify results in GENS look ok
• verify access to GENS via Scout (blocked by this: Ensure compatibility of Scout links to GENS for uploaded balsamic samples #1298 but as this issue has been linked into the feature issue for GENS (GENS #1110), I'm checking this off as this will be solved by different PRs)

Review and tests:

• Tests pass
• Code review
• New code is executed and covered by tests, and test approve

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Files	Coverage Δ
BALSAMIC/commands/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py	100.00% <100.00%> (+3.44%)	⬆️
BALSAMIC/commands/config/pon.py	100.00% <100.00%> (+4.87%)	⬆️
BALSAMIC/commands/init/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/options.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py	100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py	100.00% <100.00%> (ø)
... and 20 more

📢 Thoughts on this report? Let us know!.

[mathiasbio]

I still need to add some tests to fix the coverage but it could be nice to get some feedback at this point anyway to get ahead of the review process 🔥

[ivadym]

Amazing job with this PR and the work behind it, well done ⭐

I just left you some minor formatting and pytest suggestion

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
4 Code Smells

No Coverage information
0.0% Duplication