v2.12.1

Changed

• Reconcile workflow with wf-template v5.3.4

v2.12.0

Added

• bracken_threshold parameter to adjust bracken minimum read threshold, default 10.

Fixed

• Publish AMR results to the output directory when real time is disabled.
• Abricate process failure is now correctly caught by the workflow.

Changed

• Reconcile workflow with wf-template v5.3.3
• Update wf-metagenomics image for improved fastcat/bamstats.

v2.11.1

Fixed

• kraken2_client exits with fastcat_histogram usage error when using real time pipeline with exclude_host option.

Changed

• Reconcile template with v5.3.0 and v5.3.1
• Significantly improved the performance of report generation when summarising alignment data.

v2.11.0

Fixed

• Switch to markdown links in the outputs table in the README.
• Exclude samples if all the reads are removed during host depletion.

Added

• igv option to enable IGV in the EPI2ME Desktop Application.
• include_read_assignments option to output a file with the taxonomy of each read.
• Reads section in the report to track the number of reads after filtering, host depletion and unclassified.

Changed

• keep_bam is now only required to output BAM files.
• include_kraken2_assignments has been replaced by include_read_assignments.
• Update databases:
  • Kraken2 indexes to the ones released 2024-06-05
  • Taxonomy database to the one released 2024-09-01
• Bump to ezcharts 0.11.2

Removed

• split-prefix parameter, as the workflow automatically enables this option for large reference genomes.
• Plot showing number of reads per sample has been replaced for a new table in Reads section.

v2.10.1

Fixed

• Fix the json.decoder.JSONDecodeError when running with --amr.

v2.10.0

Changed

• The workflow now uses the fastcat read length and quality histograms instead of the per-read stats in the report process.

Added

• Output IGV configuration file if the keep_bam option is enabled and a custom reference is provided (in minimap2 mode).
• Output reduced reference file if the keep_bam option is enabled (in minimap2 mode).
• abundance_threshold reduces the number of references to be displayed in IGV.

Fixed

• Complete previous taxonomic rank when there are no parent nodes.
• Checking the correspondence between the reference and ref2taxid now also works with compressed references.
• exclude-host can input a file in the EPI2ME Desktop Application.

v2.9.4

Added

• Statistics derived from minimap2 alignment are now in the output if the keep_bam option is enabled.
• Reads below percentages of identity (min_percent_identity) and the reference covered (min_ref_coverage) are considered as unclassified in the minimap2 approach.

Fixed

• Request less memory if kraken2_memory_mapping is used.
• Show the percentage of each species when hovering over the taxonomy bar plot.

Changed

• bam folder within output has been renamed to bams.

v2.9.3

Fixed

• Files that are empty following the fastcat filtering are discarded from downstream analyses.

v2.9.2

Fixed

• "Can only use .dt accessor with datetimelike values" error in makeReport
• "invalid literal for int() with base 10" error in makeReport

v2.9.1

Fixed

• Avoid argument list lengths that may be too long when using glob patterns.
• The Kraken2 pipeline sometimes reporting wrong numbers for unclassified counts.