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

v1.0.0

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.