Replace BWA MEM with Minimap2

[standage]

This PR replaces BWA MEM with Minimap2 as the alignment program used by mhpl8r pipe. This yields substantial speedups especially for mapping to the entire genome.

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• Changes are clearly described above
• Any relevant issue threads are referenced in the description
• Any new features are tested (see the development manual for details)
• CLI documentation (see docs/cli.md) and Python API documentation (see microhapulator/api.py) are up-to-date and in sync
• Substantial changes are documented in CHANGELOG.md (see https://keepachangelog.com/en/1.0.0/)

[standage]

This command wasn't used previously because it takes so long to create a BWA index. Instead, a pre-computed index was downloaded. Constructing a Minimap2 index is much quicker and can be done as part of the CI build.