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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.

[v1.1.3]

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.

[v0.0.9]

Changed

  • per-read-stats.tsv is now produced per sample and compressed to <sample_alias>.per-read-stats.tsv.gz

[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

[v0.0.3]

Changed

  • Args parser for fastqingress
  • Set out_dir option type to ensure output is written to correct directory on Windows

[v0.0.2]

Changed

  • Tidied up docs
  • Restricting assembly to only reads that map to mpx

[v0.0.1]

First release