v0.3

• Add support for selecting hap1, hap2 as HiFiasm output
• Add support for selecting multiple HiFiasm outputs to use
• Add support for selecting a_ctg as HiFiasm output
• Add option hifiasm-write-ec, to set the --write-ec option in HiFiasm
• Include regions from the assembly that overlap, but do not match, the gene of interest
• Add separate bam file output for mapped/unmapped contigs
• Add support for selecting HiFiasm output to use via the hifiasm-output setting
• Add sample name as prefix to per-gene contigs fasta files

Full Changelog: v0.2...v0.3

v0.2

• Reorganise pipeline outputs
• Output only the best hit to the target genes for each contig
• Make both 'reference' and 'genes' inputs optional
• Add functionality for blasting genes of interest against the assembly
• Add support for multiple input bam files, see this example configuration

Initial release

v0.1

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