epi2me-labs/wf-metagenomics: 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• bracken_level parameter has been replaced by taxonomic_rank to choose the taxonomic rank at which to perform the analysis.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.