v1.3.1

Added

• --override_basecaller_cfg parameter allows users to provide a basecall configuration name in cases where automatic basecall model detection fails.
• --diff_mod option to allow users to turn off differential modified loci (DMR) and regions (DMR) analysis with DSS by setting --diff_mod false.

Changed

• Updated modkit to v0.3.0.
• Reconciled workflow _ingress.nf from wf-human-variation v2.3.1.

Fixed

• --snv crashing with --include_all_ctgs true.
• --snv always referring to model in --override_basecaller_cfg when deciding whether to call Indels.
• Automated basecaller detection not finding a basecaller model.

Removed

• --basecaller_cfg as the workflow now automatically detects the basecaller model from the input data.