fix: update read the docs for balsamic v12.0.0

[mathiasbio]

This PR:

Updates read the docs for release 12.0.0 of balsamic.

Changes in the latest release of balsamic for reference:

Added:

• PIP specific missing tools to config refactor: Fix all dependencies to specific versions #1096
• Filtering script to remove normal variants from TIDDIT feat: add TIDDIT tumor normal filtering feat: add TIDDIT tumor normal filtering  #1120
• Store TMB files in HK feat: Store TMB files in HK #1144

Changed:

• Fixed all conda container dependencies refactor: Fix all dependencies to specific versions #1096
• Changed --max_sv_size in VEP params to the size of chr1 for hg19 fix: VEP filters away variants too long to annotate #1124
• Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours fix: increase_time_for_processes #1143
• Update cosmicdb to v97 perf: COSMIC database to v97 perf: COSMIC database to v97  #1147

Fixed:

• Update cryptography version (39.0.1) due to security alert https://github.com/Clinical-- Genomics/BALSAMIC/pull/1087
• Pytest file saved in balsamic directory fix: no more pytest generated files in my directory fix: no more pytest generated files in my directory  #1093
• Fix varcall_py3 container bcftools dependency error fix: varcall_py3 container bcftools dependency error #1097

Changes in the read the docs made here:

Added:

• Descriptions of which filters were added in WGS T / N for TIDDIT normal filtering
• Update about maximum sv-size for VEP annotation

Removed:

• WGS from list of sequencing types where VarDict is used (just a correction)

Review and tests:

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

[ivadym]

Fantastic @mathiasbio 🥳

[ivadym]

Nice!

I have also spotted some erros: Dnascope is TGA and WGS, TNscope UMI is only TGA and NOT germline 🤦

In atlas is correct: https://atlas.scilifelab.se/production/data_analysis/workflows/balsamic/#data-delivery

[mathiasbio]

Nice catch, I'll make the changes!

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[codecov]

Codecov Report

Patch and project coverage have no change.

Comparison is base (7f92f66) 99.31% compared to head (80d7615) 99.31%.

Additional details and impacted files

@@               Coverage Diff               @@
##           release_12.0.0    #1153   +/-   ##
===============================================
  Coverage           99.31%   99.31%           
===============================================
  Files                  29       29           
  Lines                1756     1756           
===============================================
  Hits                 1744     1744           
  Misses                 12       12           

Flag	Coverage Δ
unittests	99.31% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.