v2.4.3

Changed

• Remove abricate version if AMR does not run.

Fixed

• Changelog format.

Added

• Alpha diversity indices: Berger-Parker dominance index, Fisher’s alpha.

v2.4.2

Changed

-Bumped minimum required Nextflow version to 23.04.2.

v2.4.1

Fixed

• Kraken2 pipeline: all the samples are shown in the report.

Changed

• Any sample aliases that contain spaces will be replaced with underscores.

v2.4.0

Added

• Antimicrobial resistance gene identification using Abricate.

v2.3.0

Added

• A new option kraken2_memory_mapping to avoid kraken2 loading the database into process-local RAM.
• --keep_bam parameter to write BAM files into the output directory (minimap pipeline).
• Lineages sunburst plot added to the report.
• SILVA.138 database available for both kraken2 and minimap2 pipelines.

Changed

• bracken_level parameter has been replaced by taxonomic_rank to choose the taxonomic rank at which to perform the analysis. It works in both pipelines.
• Updated example command displayed when running --help.
• Updated GitHub issue templates to force capture of more information.
• 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.
• Extract reads using --minimap2filter and --minimap2exclude filters. The extracted reads are in the output/filtered folder.

v2.2.1

Added

• A new option min_read_qual to filter by quality score.
• Configuration for running demo data in AWS
• AWS configuration for external kraken2_server for demonstration at LC23

Fixed

• Fix minimum and maximum length read filter.

Removed

• Default region and AWS CLI path for AWS batch profile

v2.2.0

Changed

• Updated existing databases.
• Docker will use an ARM platform image on appropriate devices.

Added

• A new PFP-8 database option.
• New test_data with Bacteria, Archaea and Fungi.

Fixed

• Fix file names when exporting tables.

v2.1.1

Fixed

• Include 'kingdom' for Eukarya.
• Add ability to use an external kraken2 server.

v2.1.0

Updated

• New fastqingress.
• New report with ezcharts.

Added

• Stacked barplot for most abundant taxa.
• Show rank information in abundance tables.
• Export function from tables.

Fixed

• Fix crash in the report with one sequence in the fastq.
• Use kraken2 with parallelization in single client.

v2.0.10

Fixed

• Remove symbolic links from store_dir.