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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[v1.2.3]

Changed

  • Reconcile workflow with wf-template v5.2.6

[v1.2.2]

Changed

  • Updated abricate container to support EPI2ME Cloud, the version of abricate remains unchanged.

[v1.2.1]

Changed

  • Reconcile workflow with wf-template v5.2.5

Fixed

  • Workflow runs to completion if flu type is undertermined
  • Bug when using custom blast_db

[v1.2.0]

Added

  • --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.

Removed

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

Changed

  • Updated Medaka to v1.12.0
  • Reconciled workflow with wf-template v5.1.4

[v1.1.0]

Changed

  • Downsampling is no longer run by default
  • Reduced test data sample size
  • Some formatting in github issue template

Fixed

  • Downsampling behaviour reworked to better catch errors from custom fasta references
  • Reports are generated when no samples have met the criteria for nextclade analysis

Added

  • RBK compatibility flag

[v1.0.1]

Changed

  • Updated docs

[v1.0.0]

Changed

  • Updated docs
  • Cloud readiness

[v0.0.11]

Changed

  • Output directory structure change
  • Adjusted size and positioning of badges to improve layout of typing table
  • Nextflow minimum version 23.04.2.

[v0.0.10]

Updated

  • Update to schema to point to cloud demo

[v0.0.9]

Changed

  • Update licence to ONT Public License
  • Made --sample_sheet an optional parameter
  • Improved Typing table in report to make typing results clearer

[v0.0.8]

Fixed

  • Poor typing performance after INSaFLU update. Rollback to version used in v0.0.6.

[v0.0.7]

Added

  • Added workflow-glue
  • Added Kit 14 test data
  • Abricate results included in the report

Changed

  • CI updates
  • Removed ping scripts
  • Update check_sample_sheet.py
  • --basecall_cfg is now used to determine a suitable Medaka model, alternatively provide the name of a model with --medaka_consensus_model to override automatic selection
  • New fastqingress implementation

Updated

  • INSaFLU v10

[v0.0.6]

Fixed

  • Updated sample sheet to expect a file

[v0.0.5]

Changed

  • Updated description in manifest

[v0.0.4]

Changed

  • Nextflow 22.08 compatibility
  • Documentation ### Removed
  • conda support

[v0.0.3]

Changed

  • Heatmap scales according to number of samples.
  • Unclassified handled separatley on report.
  • Output coverage file.

Fixed

  • Bug where if no unclassified report fails.

[v0.0.2]

Added

  • Quality score cut-off parameter.

Changed

  • Better processing of metadata.

[v0.0.1]

Added

  • First release.