feat: remove max af 1 from all workflows

[mathiasbio]

This PR:

This change has been made to remove the max allele frequency 1 filter, which has a risk of removing true somatic variants at a very high tumor purity. See issue: #1180

Removed: for now removed features.

• Removed bcftools command for setting soft-filter with maximum allele-frequency, which eventually leads to a hard removal of these variants.

Tests:

• All analysis-types completed successfully
• Few extra variants as a result of removing this filter

sequencing type	T/TN	case	# PASS variants release 13	# PASS variants this PR	# additional PASS variants	% extra PASS variants
WGS	T	civilsole	33051	33051	0	0
WGS	T	firstviper	54072	54072	0	0
WGS	TN	fleetjay	7189	7190	1	0,01%
TGA	T	setamoeba	2415	2416	1	0,04%
TGA	TN	unitedbeagle	1573	1573	0	0
TGA UMI	T (TNscope)	equalbug	158	158	0	0
TGA UMI	T (VarDict)	equalbug	70	70	0	0
TGA UMI	TN (TNscope)	uphippo	124	124	0	0
TGA UMI	TN (VarDict)	uphippo	105	105	0	0

Note that likely many variants would have been added in the T-only WGS cases if at the same time the T-only WGS specific filter bcftools filter --threads {threads} --include 'FORMAT/ALT_F1R2 > {params.strand_reads[0]} && (FORMAT/ALT_F1R2 > 0 && FORMAT/ALT_F2R1 > {params.strand_reads[0]} && FORMAT/REF_F1R2 > {params.strand_reads[0]} && FORMAT/REF_F2R1 > {params.strand_reads[0]})' --soft-filter '{params.strand_reads[1]}' --mode '+' was also removed. But as this filter also requires that some reads support a reference variant, then removing the MAX_AF 1 filter in this analysis type has no real effect.

I think we can conclude with these stats that it is safe to remove the MAX AF filter.

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 ✅

Comparison is base (f318b1e) 99.44% compared to head (a016076) 99.44%.

Additional details and impacted files

@@                 Coverage Diff                 @@
##           release_v13.0.0    #1338      +/-   ##
===================================================
- Coverage            99.44%   99.44%   -0.01%     
===================================================
  Files                   39       39              
  Lines                 1975     1974       -1     
===================================================
- Hits                  1964     1963       -1     
  Misses                  11       11              

Flag	Coverage Δ
unittests	99.44% <ø> (-0.01%)	⬇️

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[ivadym]

Looks good 💯 🎅

[sonarqubecloud]

Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
No data about Duplication

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