Compress intermediate FASTQ files

[standage]

This PR updates the end-to-end analysis workflow to compress intermediate FASTQ files and reduce storage requirements for the working directory.

Closes #188.

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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/)