New

QC

• replace multiqc report with native harpy report

Align

• BWAMEM2 has been replaced with minibwa. Long live BWA!
  • it's much faster, and takes much less time to index a reference
• coverage depth added to aggregate report for processed alignments
• minimap2 added back in (with extra perks) for long-read compatability
  • called with harpy align minimap

Report

• harpy reports can be converted to less-nice but functional standalone HTML files
  • this feature is accessed using harpy report static
  • to accomodate this, harpy report (live report website) is now harpy report live

Changes

Align

• -d (molecule distance threshold) has its default restored to 50kb since this value is used exclusively for reporting and does not alter the data

misc

• removed FASTA format validation because it can be dreadfully slow with existing tools

Report

• harpy reports can be converted to less-nice but functional standalone HTML files
  • this feature is accessed using harpy report static
  • to accomodate this, harpy report (live report website) is now harpy report live

Fixes

reports

• tables now render properly in VScode/Jupyter contexts
• xeus-python began to hang for unknown reasons and has been replaced with ipykernel

misc

• constrain CASAVA regex in FASTQ file validation so it doesn't trigger false positives when new CASAVA appears in unexpected places
• [internal] notebooks no longer a submodule/subdirectory of harpy.report
• utility check_fastq.py no longer employs globals, instead uses a sensible class system
• add multithreading to pre-workflow VCF and XAM file validation and parsing
• FASTA validation no longer checks the entire file for formatting b/c it was taking much too long on bigger genomes
  • still considering alternatives, but is disabled for now
• [internal-ish] the bwa, strobealign, and minimap2 workflows are nearly identical except for the reference preprocessing and alignment, so to minimize redundancy and duplication, those workflows have a single align.smk that imports a second snakefile align_{aligner}.smk that handles just the preprocessing and direct alignment for those aligners, then hands off to align.smk for all the downstream things (dedup, sorting, reports, etc)

Documentation

• the pages for bwa, strobealign, and minimap have been consolidated into a single page bc they are nearly identical

What's Changed

• integrate qc report natively by @pdimens in https://github.com/pdimens/harpy/pull/289
• Standalone reports by @pdimens in https://github.com/pdimens/harpy/pull/291
• Bump the dependencies group with 2 updates by @dependabot[bot] in https://github.com/pdimens/harpy/pull/293
• aligners by @pdimens in https://github.com/pdimens/harpy/pull/294

Full Changelog: https://github.com/pdimens/harpy/compare/4.1.5...4.2