Update tbprofiler v5 for structural variants

[abhi18av]

Continuing from #154 (comment)

[LennertVerboven]

@abhi18av

So I have completed most of the work on the structural variants workflow and TBProfiler V5. I still need to update the summarize_resistance.py script and will do so as soon as possible. There is currently still an issue with the structural variants as delly is ran on the bam file mapped using the -k 100 parameter which causes delly to miss structural variants. Delly should be run on a sorted, indexed and duplicate marked bam file which is mapped using the default -k parameter

[abhi18av]

@LennertVerboven , I'm doing an integration test on my side now - could you please update the Changelog.md to document the core changes.

In addition, we should include how the new database was generated

[abhi18av]

@LennertVerboven ,

The pipeline finished successfully with the new containers and here are some results from the analyses/drug_resistance/combined_variants/resistance_summaries

MTb_L1.SAMN10185847.xlsx
MTb_L3.SAMEA1877181.xlsx
MTb_L43.ERR1193883.xlsx

If these are looking fine, then please merge the PR to develop branch.