v2.0.0

What's Changed

This version provides a major speedup to SPEAR (6mins for 1000 samples on a single core) and includes the following:

-Adds SPEAR utilities module, including utilities-report to run reports on past flat file outputs, and utilities-representative to produce representative VCF files for samples from the same Pango Lineage quickly (like those used in SPEAR-Reports repo).
-Utilises Seqkit to process input fasta files, necessitating a change in fa input. All samples should be combined into a single file, which can now be gzipped to reduce overhead.
-Similarly, VCF files can now be passed to the pipeline as a single multi-sample VCF file. A helped function, utilities-vcf-merge is provided to do this merging on a directory of VCF files.
-Fixes #45 by adding the force-single flag to bcftools merge in the pipeline.

Full Changelog: v1.1.3...v2.0.0