1.10

New Features

• assembly and metassembly workflows
• --contigs option for align ... sv ... and phase workflows
• calculations for molecular coverage too
• non-singleton metrics added to alignment reports

Internal

• remove pandas dependency b/c no longer using Paramspace()
  • impute parameter file now gets transcribed into the config.yaml
• new and better validations
• some validations have progressbar and are parallelized
  • progressbar respects --quiet
• config.yaml files are written using the yaml stdlib for consistency
• workflow summaries have more robust logic

Breaking changes

• parameter file for impute has a new name column that will name relevant outputs for a given parameter set
  • this affects the output directories now, which are named according to this name value
• config.yaml file restructured a bit, mainly some params have better snake-cased names
  • skipreports is now skip under a new reports hierarchy

Pull Requests

• Add Metassembly by @pdimens in #144
• add assembly by @pdimens in #146
• Molecule coverage by @pdimens in #149
• Hotfixes by @pdimens in #150
• 151 provide harpy a list of primary autosomessex chroms for plottingreports for chromosome level assemblies by @pdimens in #152
• add quast reports to assembly by @pdimens in #155
• add singleton/non stats by @pdimens in #156

Full Changelog: 1.9...1.10