Changelog

v0.4-dev

Change default blast output from extend to hit
Add option to select type of blast output to use
Change hifiasm-flags into a list to ensure parameter value pairs are kept together
Fix a bug where the pipeline crashes if an assembly output is an empty file

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

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 bam files, see this example configuration

v0.1

Initial release

v0.0.1

Initial commit