v1.4.0

Changed

• Bump to wf-metagenomics v2.12.0

Added

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

v1.3.0

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

• Bump to wf-metagenomics v2.11.0
• keep_bam is now only required to output BAM files.
• include_kraken2_assignments has been replaced by include_read_assignments.
• Update databases:
  • Taxonomy database to the one released 2024-09-01

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.

v1.2.0

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

• exclude-host can input a file in the EPI2ME Desktop Application.

Changed

• Bump to wf-metagenomics v2.10.0

v1.1.3

Added

• Reads below percentages of identity (min_percent_identity) and the reference covered (min_ref_coverage) are considered as unclassified in the minimap2 approach.

Fixed

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

Changed

• Bump to wf-metagenomics v2.9.4
• bam folder within output has been renamed to bams

v1.1.2

Fixed

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

Changed

• Bump to wf-metagenomics v2.9.2

v1.1.1

Changed

• Bump to wf-metagenomics v2.9.1

v1.1.0

Added

• Workflow now accepts BAM or FASTQ files as input (using the --bam or --fastq parameters, respectively).

Changed

• Bump to wf-metagenomics v2.9.0
• Default for --n_taxa_barplot increased from 8 to 9.

v1.0.0

Changed

• Bump to wf-metagenomics v2.8.0
• Update docs

v0.0.4

Changed

• Bump to wf-metagenomics v2.7.0
• Fixed CHANGELOG format

v0.0.3

Changed

-Bump to wf-metagenomics v2.6.1