feat: extract additional WGS metrics

[ivadym]

This PR:

Added new WGS metrics to be extracted and stored to <case>_metrics_deliverables.yaml.

Review and tests:

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

[codecov]

Codecov Report

Merging #907 (a19323a) into develop (a80860c) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop     #907   +/-   ##
========================================
  Coverage    99.54%   99.54%           
========================================
  Files           29       29           
  Lines         1770     1775    +5     
========================================
+ Hits          1762     1767    +5     
  Misses           8        8           

Flag	Coverage Δ
unittests	99.54% <100.00%> (+<0.01%)	⬆️

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Impacted Files	Coverage Δ
BALSAMIC/constants/quality_check_reporting.py	100.00% <ø> (ø)
BALSAMIC/utils/models.py	100.00% <100.00%> (ø)
BALSAMIC/constants/common.py	100.00% <0.00%> (ø)

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[ashwini06]

Looks good 💯

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[ivadym]

Tested collect_qc_metrics.py script:

Executed command:
python collect_qc_metrics.py $output_path $multiqc_data_path $sequencing_type $capture_kit

Output file (<case>_metrics_deliverables.yaml) with the new retrieved metrics (PCT_15X, PCT_30X, PCT_60X, PCT_100X, PERCENT_DUPLICATION_R1, PERCENT_DUPLICATION_R2, MEDIAN_COVERAGE, MEAN_INSERT_SIZE):

- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R.multiple_metrics.insert_size_metrics
  name: MEAN_INSERT_SIZE
  step: multiqc_picard_insertSize
  value: 370.700624
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R.multiple_metrics.insert_size_metrics
  name: MEAN_INSERT_SIZE
  step: multiqc_picard_insertSize
  value: 379.940106
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: MEDIAN_COVERAGE
  step: multiqc_picard_wgsmetrics
  value: 39.0
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_15X
  step: multiqc_picard_wgsmetrics
  value: 0.971607
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_30X
  step: multiqc_picard_wgsmetrics
  value: 0.858525
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_60X
  step: multiqc_picard_wgsmetrics
  value: 0.008534
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_100X
  step: multiqc_picard_wgsmetrics
  value: 0.001911
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_picard_wgs_metrics.txt
  name: FOLD_80_BASE_PENALTY
  step: multiqc_picard_wgsmetrics
  value: 1.190461
  condition:
    norm: lt
    threshold: 1.8
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: MEDIAN_COVERAGE
  step: multiqc_picard_wgsmetrics
  value: 50.0
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_15X
  step: multiqc_picard_wgsmetrics
  value: 0.981034
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_30X
  step: multiqc_picard_wgsmetrics
  value: 0.911745
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_60X
  step: multiqc_picard_wgsmetrics
  value: 0.18888
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: PCT_100X
  step: multiqc_picard_wgsmetrics
  value: 0.00345
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_picard_wgs_metrics.txt
  name: FOLD_80_BASE_PENALTY
  step: multiqc_picard_wgsmetrics
  value: 1.235459
  condition:
    norm: lt
    threshold: 1.8
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_2_fastqc.zip
  name: PERCENT_DUPLICATION_R2
  step: multiqc_general_stats
  value: 15.03521942842923
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_1_fastqc.zip
  name: PERCENT_DUPLICATION_R1
  step: multiqc_general_stats
  value: 14.426654287440797
  condition: null
- header: null
  id: ACC8695A1
  input: concatenated_ACC8695A1_XXXXXX_R_2_fastqc.zip
  name: PERCENT_DUPLICATION_R2
  step: multiqc_general_stats
  value: 14.214689357571501
  condition: null
- header: null
  id: ACC8695A2
  input: concatenated_ACC8695A2_XXXXXX_R_1_fastqc.zip
  name: PERCENT_DUPLICATION_R1
  step: multiqc_general_stats
  value: 15.213739762327492
  condition: null