v1.9.0

Added

• STR workflow report now includes additional plots which display repeat units and interruptions in each supporting read
• CNV workflow now outputs an indexed VCF file to the output directory

Changed

• Legend symbols in STR genotpying plot
• Unambiguous naming of bedMethyl files generated with --mod
  • Unphased outputs will have the pattern [sample_name].wf_mods.bedmethyl.gz
  • Phased outputs will have the pattern [sample_name]_[1|2|ungrouped].wf_mods.bedmethyl.gz

Fixed

• Report step failing if bcftools stats file has only some sub-sections
• Clair3 ignoring the bed file
• merge_haplotagged_contigs incorrectly generating intermediate CRAM when input is BAM
• STR content generation failing due to forward slash in disease name in variant_catalog_hg38.json
• Report name for the read alignment statistics now follows the pattern [sample_name].wf-human-alignment-report.html