v1.7.2

This is a re-release of v1.7.1 with support for MinKNOW integration.

Changed

• Added MinKNOW support to workflow schema.

v1.7.1

Changed

• Reconciled workflow with wf-template v5.3.4.
• Report wording to correctly reflect order of host filtering and downsampling.

v1.7.0

Added

• Support for host_reference and regions_bedfile columns in the sample sheet (to provide different references for individual samples). Sample sheet specification cannot be used in conjunction with --host_reference and --regions_bedfile parameters.
• Host reference BAM and BAI are now published in outputs.

v1.6.0

Added

• Expected reference and insert columns added to the sample status table with a tick or cross indicating if the assembly is as expected based on the provided reference.
• --expected_identity parameter to define the minimum expected identity percentage between provided references and the assembly (default: 99).
• --expected_coverage parameters for define the minimum expected coverage percentage between a provided reference and the assembly (default: 95).
• Insert QC section with coverage and BLAST Identities for Insert if an insert reference is provided.

Changed

• Assembly reorientation attempted so that it starts at full_reference start position and matches the direction, when --full_reference is provided.
• Demo has been updated to include 12 samples.
• Emit mafs to enable dot plots to be re-used in reports generated in aliased workflows.

v1.5.0

Fixed

• Parsing of an insert that is split between the start and end of the assembly and is a reverse complement.
• Swap read count plot axis so Sample aliases are readable.
• Incorrectly running Insert QC and outputting Insert statistics when an insert was not present in the assembly.

Changed

• Updated Medaka to v2.0.0
• The default maximum allowed mismatches in the insert primers has changed from 3 to 2.

v1.4.0

Added

• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.
• --medaka_model_path parameter to provide a custom medaka model. This is intended for users testing experimental Medaka models and will not be needed for general use.

Removed

• The now redundant --basecaller_cfg parameter as its value is now automatically detected from the input data on a per-sample basis.

Changed

• Min and max read length determined per sample based on approx_size
• Emit assembly quality stats as part of final workflow outputs
• Trim length parameter can be set to 0.

v1.3.1

Added

• Parameter to control number of mismatches allowed in cutsite analysis

Fixed

• Regression causing incorrect raw read counts shown in "Read stats" section of the report.
• INDELS now called from assembly to reference alignment (-m1 added to bcftools mpileup)

v1.3.0

Changed

• Updated Medaka to v1.12.0.
• Updated EZCharts to v0.10.0.

Added

• --full_reference parameter to accept a reference of the full construct. If provided, an additional construct QC section will be output in the report which will include reference coverage and percentage identity per sample.
• Additional per-sample output files if --full_reference is provided:
  • BAM: Reference aligned with the assembly in an indexed BAM.
  • Variant stats: BCF stats report with any variants found between reference and assembly.
  • Variant BCF: BCF file with all variants found between reference and assembly.
  • BAM stats: Stats report from alignment of provided reference with assembly.
• Optional linearisation efficiency section in the report, added when the cut_site column is supplied in the sample sheet.
• Support for full_reference and insert_reference columns in the sample sheet (to provide different references for individual samples). The MSA for insert analysis will group samples based on insert_reference.
• Workflow now additionally accept BAM as input by using the --bam parameter.

Fixed

• Update plannotate version to v1.2.2 which fixes error that occurs when a feature contains a float.

Removed

• The --medaka_model parameter (since the appropriate Medaka model is now automatically determined from the input data). If the input data are lacking information on the model that was used to basecall them, the basecall model must be provided with --basecaller_cfg. Otherwise the workflow will fail.

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).