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.
Flyestats output and report
- Reconciled workflow with wf-template v5.3.0
- Filtering samples with no data on meta.n_seqs instead of presence of fastq file post ingress
- Reconciled workflow with wf-template v5.2.5.
- Report wording.
- Updated Medaka to v2.0.0.
- Workflow now accepts BAM as well as FASTQ files as input (using the
--bamor--fastqparameters, respectively) --override_basecaller_cfgparameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.
- The
--basecaller_cfg,--medaka_consensus_model, and--medaka_variant_modelparameters as the appropriate Medaka model is now automatically determined from the input data.
client_fieldsparameter to allow input of a JSON file of key value pairs to display on output reports.min_read_lengthparameter to remove reads below specified length (default 1000bp) from downstream analysis, to improve de novo assembly process- Salmonella serotyping with
SeqSero2
- Duplicate entries in
Pointfinderprocessing
- Report generation when
Resfinderfails
- Sample results aggregated into
results.json flye_genome_sizeandflye_asm_coverageparameters for controlling the initial downsampling step before the de novo assembly
- De novo assembly mode uses
--nano-hqrather than--nano-raw - Some formatting in github issue template.
- Retry and memory bump if de novo assembly fails first time
- Workflow now runs to completion when a sample fails the de novo assembly
- The workflow requesting too little memory for some processes.
- FASTA now includes basecaller model in headers
- Updated to most recent version of Medaka container.
- Minimum compute requirements
- Cloud support for the workflow within the EPI2ME Application.
- Documentation
- MacOS ARM64 support
- New parameter
--flye_optsfor passing additional arguments toflye.
- Clarify docker is default in README
- De novo assembly failing due to low coverage in some situations.
- Overwrites in Nextflow config implemented incorrectly
- Updated Medaka to 1.9.1.
- Edge case where medaka variant output is unsorted and causes medaka annotate to exit
- Bumped minimum required Nextflow version to 23.04.2.
- Now uses Medaka v1.8.2 with updated models.
- Options for the
--basecaller_cfgparameter were updated. The default is now[email protected].
- 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
- Isolate single sample reports
- Include disinfectant resistance results in the report.
- MLST core gene analysis added to
--isolatesparameter.
speciesparameter is removed, valid pointfinder species will be inferred from MSLT results.- In case
flyefails 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
--helpoutput - Enum choices are enumerated as part of the error message when a user has selected an invalid choice
- Replaced
--threadsoption in fastqingress with hardcoded values to remove warning about undefinedparam.threads
--isolatesparameter that will run the ResFinder tool on the final assembly to output antimicrobial resistance genes.- Configuration for running demo data in AWS
- Report is now created with
ezcharts.
- Rows with too few / too many columns in
medaka_models.tsv. - Check sample sheet script.
- Now uses new
fastq_ingressimplementation.
- Medaka models added to container
- QUAST
--basecall_cfgis now used to determine suitable Medaka model, alternatively provide the name of a model with--medaka_consensus_modeland--medaka_variant_modelto override automatic selection.
- sample_sheet format in schema to expect a file
- Updated description in manifest
- Output QUAST stats for reference and denovo based assembly
- Replace QUAST with MetaQUAST
- Add species ID to run summary table
- For reference based assembly
--reference_based_assemblyparameter should now be provided with a--reference. The default is to use denovo assembly. - Tidy up presentation in report
-profile condais no longer supported, users should use-profile standard(Docker) or-profile singularityinstead- Docs update
nextflow run epi2me-labs/wf-bacterial-genomes --versionwill now print the workflow version number and exit
- Prokka only runs in denovo assembly mode
- Tidy up report code
- Added QUAST for assembly stats
- Remove sanitize option
- Update syntax to fix reference error
- Better help text on cli
- Fastqingress metadata map
- Use groovy script to ping after workflow has run
- Output medaka vcf
- Remove reliance on simpleName
- Amend report name.
- Add read me docs.
- Option to add suffix to HTML report name.
- Visualisation of prokka output.
- Choice of de novo assembly or alignment.
- Supports multibarcodes
- Medaka version.
- Depth coverage graphs.
- Use mosdepth and fastcat.
- Update project with latest practices from wf-template.
- Use
mambaby default when using conda profile.
- Incorrect specification of conda environment file location.
- Rework workflow to use new medaka methodology for improved robustness of results.
- Standardised report name.
- Resolved confusion between documentation and workflow: workflow now requires a directory as input.
- aplanat import error
- Prokka can be optionally run to annotate consensus sequence.
- Variant call summary produced using aplanat report component.
- Initial release
- Basic running of medaka variant calling and report.