perf: Parallelize download reference

[fevac]

This PR:

Fixes #1064

Changed: parallelize download of reference files

How to tests:

• Dry-run of balsamic init --outdir $path2balsamic_cache --cosmic-key "${COSMIC_KEY}" --genome-version hg19 --run-mode local --snakemake-opt "--cores 36" --container-version develop
• Make sure that download_reference is set for multiple executions (count > 1)
• Run of balsamic init --outdir $path2balsamic_cache --cosmic-key "${COSMIC_KEY}" --genome-version hg19 --run-mode local --snakemake-opt "--cores 2 --until download_reference" --container-version develop -r

Review and tests:

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

[fevac]

Tests output:

• balsamic init --outdir path2balsamic_cache --cosmic-key "${COSMIC_KEY}" --genome-version hg19 --run-mode local --snakemake-opt "--cores 36" --container-version develop

• balsamic init --outdir path2balsamic_cache --cosmic-key "${COSMIC_KEY}" --genome-version hg19 --run-mode local --snakemake-opt "--cores 2 -R download_reference --until download_reference" --container-version develop -r

• balsamic init --outdir path2balsamic_cache --cosmic-key "${COSMIC_KEY}" --genome-version hg19 --run-mode local --snakemake-opt "--cores 2 --until download_reference" --container-version develop -r
  OBS: I skipped the download of gnomad.genomes.r2.1.1.sites.vcf.bgz as the file is huge and takes a long time.
  

[codecov]

Codecov Report

Base: 99.25% // Head: 99.25% // No change to project coverage 👍

Coverage data is based on head (029dc6c) compared to base (491b04c).
Patch has no changes to coverable lines.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1065   +/-   ##
========================================
  Coverage    99.25%   99.25%           
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  Files           29       29           
  Lines         1755     1755           
========================================
  Hits          1742     1742           
  Misses          13       13           

Flag	Coverage Δ
unittests	99.25% <ø> (ø)

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[ivadym]

Nice 🔥

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[fevac]

@ivadym thank you for the review 🌟 Tests on hasta are working, should I merge into develop?

[ivadym]

Sure, go ahead. It's a good first step to start addressing this issue: #1044