v1.3.0

Added

• Workflow now accepts BAM as well as FASTQ files as input (using the --bam or --fastq parameters, respectively)
• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.

Removed

• The --basecaller_cfg, --medaka_consensus_model, and --medaka_variant_model parameters as the appropriate Medaka model is now automatically determined from the input data.

Changed

• New docker images for resfinder and mlst.
• Updated Medaka to v1.12.0.
• Updated minimum computer specs as flye was not performing robustly.