feat: analysis workflow option

[ashwini06]

This PR:

Is the duplicate of #932, where the base branch develop is corrupted which resulted in the codecov issues

Fixes: #896

• Adds new analysis_workflow option to balsamic config case to run different workflows (balsamic, balsamic-umi)
• If --analysis-workflow=balsamic run only balsamic workflow, else if --analysis-workflow=balsamic-umi runs both balsamic+UMI workflow

Test CommandLine

# create config json for balsamic only analysis

balsamic config case  --analysis-workflow balsamic --case-id TN_panel_balsamic --analysis-dir run_tests/ --balsamic-cache /home/proj/stage/cancer/balsamic_cache/ -t tests/test_data/fastq/S1_R_1.fastq.gz -n tests/test_data/fastq/S2_R_1.fastq.gz -p tests/test_data/references/panel/panel.bed

balsamic run analysis -s run_tests/ TN_panel_balsamic/TN_panel_balsamic.json

# create config json for balsamic+UMI  analysis

balsamic config case  --analysis-workflow balsamic-umi --case-id TN_panel_balsamic_umi --analysis-dir run_tests/ --balsamic-cache /home/proj/stage/cancer/balsamic_cache/ -t tests/test_data/fastq/S1_R_1.fastq.gz -n tests/test_data/fastq/S2_R_1.fastq.gz -p tests/test_data/references/panel/panel.bed 

balsamic run analysis -s run_tests/TN_panel_balsamic_umi/TN_panel_balsamic_umi.json

Changed:

• UMI-workflow for panel cases to be run only with balsamic-umi
• only BALSAMIC workflow will be run by balsamic

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

Merging #937 (66e20eb) into develop (0c6ee47) will decrease coverage by 0.34%.
The diff coverage is 98.94%.

@@             Coverage Diff             @@
##           develop     #937      +/-   ##
===========================================
- Coverage    99.60%   99.26%   -0.35%     
===========================================
  Files           29       29              
  Lines         1761     1758       -3     
===========================================
- Hits          1754     1745       -9     
- Misses           7       13       +6     

Flag	Coverage Δ
unittests	99.26% <98.94%> (-0.35%)	⬇️

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

Impacted Files	Coverage Δ
BALSAMIC/commands/config/pon.py	95.12% <ø> (ø)
BALSAMIC/commands/init/base.py	100.00% <ø> (ø)
BALSAMIC/commands/report/deliver.py	100.00% <ø> (ø)
BALSAMIC/constants/qc_metrics.py	100.00% <ø> (ø)
BALSAMIC/constants/reference.py	100.00% <ø> (ø)
BALSAMIC/constants/variant_filters.py	100.00% <ø> (ø)
BALSAMIC/constants/workflow_params.py	100.00% <ø> (ø)
BALSAMIC/constants/workflow_rules.py	100.00% <ø> (ø)
BALSAMIC/utils/qc_metrics.py	100.00% <ø> (ø)
BALSAMIC/commands/run/analysis.py	99.05% <50.00%> (-0.95%)	⬇️
... and 9 more

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[ashwini06]

balsamic dry-runs

For Tonly_panel (Balsamic_only)

For Tonly_panel (Balsamic + UMI)

For TN_panel (Balsamic only)

For TN_panel (Balsamic+UMI)