v2.14.1

This patch release of wf-metagenomics updates the AMR container image to ensure the workflow can be correctly executed on computers with ARM processors. Users do not need to adopt this release unless they are using the workflow on a computer with an ARM processor and make use of the AMR options.

Fixed

• Updated Abricate Docker image to natively support ARM processors.

v2.14.0

This minor release of wf-metagenomics fixes issues with missing files and zero divisions experienced when the coverage of input data is very low.
This version of wf-metagenomics also removes the real time analysis options in order to simplify the workflow.
New solutions for real time taxonomic classification are in development but users who wish to continue using this functionality will need to pin wf-metagenomics v2.13.0.

Changed

• Updated to wf-template v5.6.2, changing:
  • Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress.
  • Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs.
  • pre-commit configuration to resolve an internal dependency problem with flake8. This has no effect on the workflow.
• Values in the diversity table appear as None if there are no reads in the sample.
• Values in the abundance table are now integers instead of floats.
• Samples with fewer than 50% of the median read count across all samples are excluded from the rarefaction table. This is to avoid the rest of the samples being rarefied to a very low number of reads, which would lead to a loss of information.

Fixed

• Updated to wf-template v5.6.2, fixing:
  • Sequence summary read length N50 incorrectly displayed minimum read length, it now correctly shows the N50.
  • Sequence summary component alignment and coverage plots failed to plot under some conditions.
• Missing output file containing per-read assignments after identity and coverage filters when using include_read_assignments with the minimap2 subworkflow; this table is now correctly published to {alias}_lineages.minimap2.assignments.tsv.
• Missing output file(s) encountered in the prepare_databases:determine_bracken_length process when using the bracken_length option.
• Missing output file(s) encountered in the minimap_pipeline:getAlignmentStats process when all reads are unclassified.
• pandas.errors.EmptyDataError encountered in the getAlignmentStats process when reference coverage does not reach 1x
• ZeroDivisionError: division by zero encountered in the progressive_bracken process when there are no taxa identified at all.
• Versions of some tools were not properly displayed in the report.
• raise ValueError("All objects passed were None") caused by all samples containing zero classified reads after applying bracken threshold.

Removed

• Real time functionality has been removed to simplify the workflow. The following parameters have been removed as they are no longer required: server_threads, kraken_clients, port, host, external_kraken2, batch_size, real_time, read_limit. Using these parameters in v2.14.0 onwards will cause an error.
• Update image to remove kraken2-server dependency as it was only required by the real time workflow.

v2.13.0

Changed

• Update Seqkit version(>2.6.0) so Abricate can handle bgzip files without decompressing.
• Split taxonomy classification from minimap2 alignment process to make it more modular.
• Update databases:
  • Kraken2 indexes to the ones released 2024-12-28
  • NCBI Taxonomy database updated to the one released 2025-01-01
• Reconciled workflow with wf-template v5.5.0.

Added

• Table with alignment stats is now an output: alignment_tables/{{ alias }}.alignment-stats.tsv
• output_unclassified parameter to output FASTQ with unclassified sequences for both minimap2 and kraken2 modes (default: False).

Fixed

• Fix error: bracken-build: line 231: syntax error: unexpected end of file when using SILVA database.

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.