New features

• naibr variant calling now relies on whatshap to back-phase BAM files from a phased VCF for much, much better variant calling
• harpy preflight to do a full suite of file format validations on bam/fastq files prior to running one of the main modules
• lots more file-check validations and helpful error messages before harpy hands things over to snakemake
• regular RMarkdown reports have been completely revised using R::Flexdashboard

bugfixes

• More file checks means fewer downstream errors
• typos corrected

breaking changes

TL;DR: This release pretty much breaks every aspect of the the previous APIs. Pretend you've never used Harpy before

• no more --method flag, instead methods have been submodule-arized into
  • harpy align --method bwa ... is now harpy align bwa ...
  • harpy align --method ema... is now harpy align ema ....
  • harpy variants snp --method... is now harpy snp method .... (method = freebayes or mpileup)
  • harpy variants sv --method...is nowharpy sv method ....(method =leviathanornaibr`)
• harpy extra has been made into submodules too, now making:
  • harpy popgroup to create the popgroup file
  • harpy stitchparams to create the STITCH parameter file
  • harpy hpc to create a SLURM hpc profile