v0.2.0

Added

• An experimental methylation subworkflow has been integrated, using modbam2bed to aggregate modified base counts (input BAM should have MM and ML tags), enable this with --methyl

Changed

• Workflow experimentally supports CRAM as input, uBAM input uses CRAM for intermediate files
• Reference FAI is now created if it does not exist, rather than raising an error
• --sniffles_args may be used to provide custom arguments to the sniffles2 process
• Output files are uniformly prefixed with --sample_name

Fixed

• Existence of Clair3 model directory is checked before starting workflow
• --GVCF and --include_all_ctgs are correctly typed as booleans
  • --GVCF now outputs GVCF files to the output directory as intended
  • --include_all_ctgs no longer needs to be set as --include_all_ctgs y