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@pdimens pdimens released this 27 Oct 15:41
· 1223 commits to main since this release
0.4.0
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Learn about vigilant mode.

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

paint and polish

  • error messages now use rich (which was always available) to provide really nice and organized output
  • rmarkdown html now uses flexdashboard

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
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