v0.4.0

Added

• Documentation updated to include workflow steps.
• Full plasmid assembly mean quality table in report.
• Output a fastq of the final assembly.
• Insert reference, if provided, will now be used to variant call insert consensus with bcftools.

Removed

• Unused packages from the container.

Changed

• Enum choices are enumerated in the --help output
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice
• Bumped minimum required Nextflow version to 22.10.8
• Updated GitHub issue templates to force capture of more information.
• Reference parameter changed to --insert_reference.
• Updated example command displayed when running --help
• Parameter--approx_size_sheet no longer accepted, instead use sample sheet with optional additional column approx_size.
• Any sample aliases that contain spaces will be replaced with underscores.

Fixed

• Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads
• Annotation output bed file has correct notation for strand.