harpy v0.8.0

Changes

Under the hood

• snakemake updated to v8.x
• all snakemake code updated for v8
• conda python env is now 3.12 (snakemake dependency)
• pysam removed from conda recipe, now exists in align runtime environment
• conditional rules in snakefiles are cleaner and more idiommatic

Usage

• option --print-only still exists, but is now hidden since it's only really used in development and kinda rarely at that
• BIG FEATURE new --output-dir (-o) option for all main modules to specify an output directory
  • BREAKING CHANGE the output directories for all the modules are identical to the previous versions except
    • harpy snp defaults to SNP/method output directory
    • harpy sv defaults to SV/method output directory

Bugs fixed

• Some help string language improvements
• mpileup with --populations now correctly uses the population mode (it accidentally ignored it)

Full Changelog: 0.7.0...0.8.0