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.
--isolates
parameter 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_ingress
implementation.
- Medaka models added to container
- QUAST
--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.
- 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_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
nextflow run epi2me-labs/wf-bacterial-genomes --version
will 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
mamba
by 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.