v2.0.0: Optimized MAGMA pipeline with NTM support

What's Changed

• Add MTB_L10 reference in the bundled GVCF by @abhi18av in #200
• Iteration for v2.0.0-beta release - update GVCF by @abhi18av in #201
• Remove the custom built who-magma database for tb-profiler by @abhi18av in #203
• Improve strand bias filter for minor/infrequent variants by @abhi18av in #202
• Simplify the samplesheet by @abhi18av in #204
• Compute FASTQ stats from the input samplesheet by @abhi18av in #205
• Enable the ITOL annotations in the tb-profiler command by @abhi18av in #197
• Add clarification for bqsr recaliberated files by @abhi18av in #213
• Structural variants v2 - accommodate transposable elements by @abhi18av in #209
• Update convert_ismapper_to_vcf.py by @vrennie in #214
• Iteration for 2.0.0-beta release by @abhi18av in #206

Full Changelog: v2.0.0-alpha...v2.0.0-beta