fix: add postprocess bam and memory to vardict

[mathiasbio]

This PR:

This PR aims to solve the issue in VarDict randomly crashing with the mysterious memory issue: #1286

Tests:

• It has been run 12 times on the same TGA T/N case that usually fails 1 out of 6 times, and succeeded in all attempts.
• downsampled WGS T/N case runs without errors
• TGA T/N umi case runs without errors

Added:

• Picard AddReadGroup command before VarDict
• Samtools sort and index after merging reads with Sentieon Dedup

Changed: for changes in existing functionality.

• Increased memory and threads for VarDict

Review and tests:

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

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (a08f380) 99.43% compared to head (7b912c7) 99.43%.

Additional details and impacted files

@@               Coverage Diff                @@
##           release_v13.0.0    #1332   +/-   ##
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  Coverage            99.43%   99.43%           
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  Files                   38       38           
  Lines                 1962     1962           
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  Hits                  1951     1951           
  Misses                  11       11           

Flag	Coverage Δ
unittests	99.43% <100.00%> (ø)

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[fevac]

@mathiasbio this is really great. As far as I can see, this PR:

• Increases memory for Vardict
• Filter bam files by only keeping mapped reads
• Changes readgroup in bam files

I guess you don't know what is actually solving the issue?

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[mathiasbio]

All tests succeed! So I will squash and merge this 🌟

[mathiasbio]

And yes! Exactly, I still don't know why it's happening or why this seems to have solved the issue 😬