v1.1.3

Fixed

• Updated recommended (32GB) and minimum (16GB, with --assembly false) memory requirements.

Changed

• Reconcile workflow with wf-template v5.2.6.

v1.1.2

Changed

• Reconcile workflow with wf-template v5.2.5.

Fixed

• Show Nextclade version in software versions table.

v1.1.1

Added

• Nextclade typing for both reference-based and optional de novo consensus assemblies.
• Clade I reference sequence (NC_003310.1) is now available for selection.

Changed

• Default reference sequence changed to NC_003310.1 (Clade I) following mpox PHEIC announcement.

v1.1.0

Added

• Support for uBAM (unaligned BAM) input files.
• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.

Changed

• Now checks if input BAM files have been aligned against the selected reference.
• Updated Medaka to v1.12.0.

Removed

• The --medaka_options parameter as the appropriate Medaka model is now automatically determined from the input data.

v1.0.0

Added

• Workflow can now take either a BAM file or FASTQ file as input.

Changed

• Improved Medaka speed on ARM processors.
• Updated documentation format.

Fixed

• Parameter to turn off assembly has been fixed.

v0.0.8

Changed

• Bumped minimum required Nextflow version to 23.04.2.
• 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.
• Updated GitHub issue templates to force capture of more information.
• Example command to use demo data.
• Spaces in sample aliases are now replaced with underscores.
• Deprecated parameter process_label.

v0.0.7

Changed

• Updated whole workflow to bring up-to-date with recent template changes

Added

• Configuration for running demo data in AWS

v0.0.6

Changed

• Updated description in manifest

v0.0.5

Removed

• conda support

Changed

• Updating templates
• Documentation

Fixed

• Fix for error with empty VCF files (@MarieLataretu)

v0.0.4

Added

• Minimum coverage parameter