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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.

[v1.2.0]

Added

  • client_fields parameter to allow input of a JSON file of key value pairs to display on output reports.
  • min_read_length parameter to remove reads below specified length (default 1000bp) from downstream analysis, to improve de novo assembly process
  • Salmonella serotyping with SeqSero2

Fixed

  • Duplicate entries in Pointfinder processing

[v1.1.1]

Fixed

  • Report generation when Resfinder fails

[v1.1.0]

Added

  • Sample results aggregated into results.json
  • flye_genome_size and flye_asm_coverage parameters for controlling the initial downsampling step before the de novo assembly

Changed

  • De novo assembly mode uses --nano-hq rather than --nano-raw
  • Some formatting in github issue template.
  • Retry and memory bump if de novo assembly fails first time

Fixed

  • Workflow now runs to completion when a sample fails the de novo assembly
  • The workflow requesting too little memory for some processes.

[v1.0.2]

Added

  • FASTA now includes basecaller model in headers

Changed

  • Updated to most recent version of Medaka container.

[v1.0.1]

Changed

  • Minimum compute requirements

[v1.0.0]

Added

  • Cloud support for the workflow within the EPI2ME Application.

Changed

  • Documentation

[v0.4.0]

Added

  • MacOS ARM64 support
  • New parameter --flye_opts for passing additional arguments to flye.

Changed

  • Clarify docker is default in README

Fixed

  • De novo assembly failing due to low coverage in some situations.

[v0.3.3]

Fixed

  • Overwrites in Nextflow config implemented incorrectly

Changed

  • Updated Medaka to 1.9.1.

[v0.3.2]

Fixed

  • Edge case where medaka variant output is unsorted and causes medaka annotate to exit

Changed

  • Bumped minimum required Nextflow version to 23.04.2.
  • Now uses Medaka v1.8.2 with updated models.
  • Options for the --basecaller_cfg parameter were updated. The default is now dna_r10.4.1_e8.2_400bps_sup@v4.2.0.

[v0.3.1]

Changed

  • GitHub issue templates
  • Output GFF and GBK files from Prokka
  • Updated resfinder version to 4.3.2
  • Removed mutation of unknown effect in SNP-mediated AMR genes output

[v0.3.0]

Added

  • Isolate single sample reports
  • Include disinfectant resistance results in the report.
  • MLST core gene analysis added to --isolates parameter.

Changed

  • species parameter is removed, valid pointfinder species will be inferred from MSLT results.
  • In case flye fails due to low coverage, the workflow will continue and this will be indicated in the report.
  • Bumped minimum required Nextflow version to 22.10.8
  • 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

Fixed

  • Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads

[v0.2.14]

Added

  • --isolates parameter that will run the ResFinder tool on the final assembly to output antimicrobial resistance genes.
  • Configuration for running demo data in AWS

Changed

  • Report is now created with ezcharts.

[v0.2.13]

Fixed

  • Rows with too few / too many columns in medaka_models.tsv.
  • Check sample sheet script.

Changed

  • Now uses new fastq_ingress implementation.

[v0.2.12]

Fixed

  • Medaka models added to container

Removed

  • QUAST

[v0.2.11]

Changed

  • --basecall_cfg is now used to determine suitable Medaka model, alternatively provide the name of a model with --medaka_consensus_model and --medaka_variant_model to override automatic selection.

[v0.2.10]

Fixed

  • sample_sheet format in schema to expect a file

[v0.2.9]

Changed

  • Updated description in manifest

[v0.2.8]

Changed

  • Output QUAST stats for reference and denovo based assembly

[v0.2.7]

Changes

  • Replace QUAST with MetaQUAST
  • Add species ID to run summary table
  • For reference based assembly --reference_based_assembly parameter should now be provided with a --reference. The default is to use denovo assembly.
  • Tidy up presentation in report
  • -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
  • Docs update

Added

  • nextflow run epi2me-labs/wf-bacterial-genomes --version will now print the workflow version number and exit

Fixes

  • Prokka only runs in denovo assembly mode
  • Tidy up report code

[v0.2.6]

Changes

  • Added QUAST for assembly stats
  • Remove sanitize option

Fixes

  • Update syntax to fix reference error

[v0.2.5]

Changes

  • Better help text on cli
  • Fastqingress metadata map
  • Use groovy script to ping after workflow has run

Fixes

  • Output medaka vcf
  • Remove reliance on simpleName

[v0.2.4]

Fixed

  • Amend report name.

[v0.2.3]

Added

  • Add read me docs.

[v0.2.2]

Added

  • Option to add suffix to HTML report name.
  • Visualisation of prokka output.
  • Choice of de novo assembly or alignment.
  • Supports multibarcodes

Updated

  • Medaka version.
  • Depth coverage graphs.
  • Use mosdepth and fastcat.

[v0.2.1]

Changed

  • Update project with latest practices from wf-template.
  • Use mamba by default when using conda profile.

Fixed

  • Incorrect specification of conda environment file location.

[v0.2.0]

Changed

  • Rework workflow to use new medaka methodology for improved robustness of results.

[v0.1.3]

Changed

  • Standardised report name.

[v0.1.2]

Fixed

  • Resolved confusion between documentation and workflow: workflow now requires a directory as input.

[v0.1.1]

Fixed

  • aplanat import error

[v0.1.0]

Added

  • Prokka can be optionally run to annotate consensus sequence.

Changed

  • Variant call summary produced using aplanat report component.

[v0.0.1]

  • Initial release

Added

  • Basic running of medaka variant calling and report.