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• include_kraken2_assignments has been replaced by include_read_assignments.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.