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