v1.2.0

Added

• Reinstate Canu assembler alongside Flye.
• --assembly_tool parameter with options canu and flye (default: flye).
• --client_fields parameter to add extra info to the report

v1.1.0

Changed

• Ensure repetitive regions are marked on the dot plot by reducing the threshold for suppressing repeats inside exact matches.

Added

• --large_construct parameter for assembly of larger constructs including Bacterial Artificial Constructs(50,000-300,000bps).

v1.0.0

Removed

• Parameters --min_barcode and --max_barcode
• Default local executor CPU and RAM limits.

Changed

• Parameterised Flye meta option (--non_uniform_coverage) for non-uniform data and defaulted to false.

Fixed

• Now handles sample aliases consisting only of numbers.

v0.5.3

Fixed

• Squashed assembly stats section downsampled plots.

Added

• Log a warning when sample sheet approx size column is being used instead of approx size parameter.

v0.5.2

Fixed

• Deconcatenate only if the assembly is not of the approx. expected size.
• .gbk output file has the actual sequence for the origin

Added

• Dotplot allowing to visualize the repetitive regions in assemblies.
• If approximate size is <=3000 set Flye min overlap to 1000.

v0.5.1

Added

• Additionally output plannotate annotations as a GenBank (.gbk) file.

Removed

• Remove plasmid length column from plannotate feature table.

Changed

• Strand column of plannotate feature to use + and - notation.
• Default --primers parameter is now set to null.

Fixed

• If --host_filter provided the fastcat stats will be included in the report.

v0.5.0

Changed

• The report has been updated and re-ordered to improve usability.
• Default basecaller cfg is now dna_r10.4.1_e8.2_400bps_sup@v4.2.0.
• Docker will use an ARM platform image on appropriate devices.

Fixed

• Updated basecaller cfg model options.
• Workflow will still output report if there are no assemblies.

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.

v0.3.1

Added

• Configuration for running demo data in AWS

v0.3.0

Added

• Flye replaces canu as the assembler tool.