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@pdimens pdimens released this 20 May 15:52
· 160 commits to main since this release
3.0
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Learn about vigilant mode.

This release has SO MANY breaking changes. It's absolutely not backwards compatible in any way whatsoever.

Breaking changes

  • re-implementation of ordering iteration within OrderMarkers2 rather than externally
    • no more need for multiple files per ordering iteration
    • no more need to find best likelihoods
  • removal of best-finding rules
  • summary scripts changed to accommodate change above
  • folder naming structure now sequential
  • LepMap3 and LepAnchor deps now in software folder
  • config.yaml has new params, dropped threads_per
  • Snakefile now named LepMap3.smk

New Features

  • LepAnchor support now included. Batteries included!
    • Automates repeat-masking and chainfile creation (the worst parts of the process)
  • The plots created by the scripts (like Trim/QA plots) are a LOT nicer and more descriptive
  • iteration mechanics now make the pipeline even more flexible and there are fewer performance bottlenecks (faster!)

Fixes

  • SeparateChromosomes2 summarization wasn't working correctly and replaced by a bulletproof R script
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