nf-core/viralmetagenome: v1.2.0 - Damson Dove

v1.2.0 - 2026-09-16 Added (#312) - Fix #282 - drop unmapped reads from the contig-coverage alignment and unmapped read pairs from the alignments used in polishing and consensus refinement, and add param --keep_unmapped to carry them through instead (by @Joon-Klaps) (#313) - Add param --normalise_reads to digitally normalise reads with BBNorm before de novo assembly (by @Joon-Klaps) (#317) - Add tests/lib/UTILS.groovy and rewrite the pipeline-level nf-tests as scenario lists, so assertions are defined once instead of copied across seven files (by @Joon-Klaps) (#318) - Document how to build a custom annotation database from NCBI Virus, and fix stale customisation/databases.md cross-references left over from a docs restructure (by @Joon-Klaps) (#318) - Add param --annotation_metadata to read the consensus annotation fields from a csv/tsv table (optionally gzipped) instead of parsing them out of the annotation database fasta headers (by @Joon-Klaps) (#319) - Add a "Contig Taxonomy" MultiQC bar chart summarising contig taxonomic classifications (species/taxon level, per sample), switchable between all clusters and only the reconstructed ones, plus a separate genome-completeness heatmap (by @Joon-Klaps) (#320) - Fix #281 - add opt-in param --use_host_filtered_reads to route host-filtered reads into the iterative consensus refinement and final variant-calling mapping steps. Defaults to false to preserve existing behaviour (by @Joon-Klaps) (#321) - Template update to nf-core/tools v4.1.0. The lint workflow pins Nextflow to 25.10.7 until nextflow-io/nextflow#7474 ships in a 26.04.x release (by @Joon-Klaps) (#322) - Update all nf-core modules and subworkflows (by @Joon-Klaps) Fixed (#302) - Fix #285 & update modules of the subworkflow fastq_kraken_kaiju (by @Joon-Klaps) (#315) - Fix #314 - make cluster.tsv not an 'intermediate' file, as it contains a lot of info and is useful for downstream analyses (by @Joon-Klaps) (#322) - Replace the deprecated cat/cat module with find/concatenate, and tabix/tabix module with htslib/bgziptabix (by @Joon-Klaps) (#324) - Release fixes: pin Python 3.11 in the quast conda environment (distutils was removed in Python 3.12+), pin Nextflow 25.10.7 in the download-test workflow (same nextflow-io/nextflow#7474 workaround as the lint workflow), make the pipeline_info pre-commit hook inspect only staged paths, and warn instead of crash on an unparsable --annotation_metadata table (by @Joon-Klaps) (#326) - Fix #296 - params.* are now read only in the root main.nf and passed down as explicit take: inputs; workflows/ and subworkflows/local/ no longer reference the global params object (by @Joon-Klaps) Dependencies | Dependency | Old version | New version | | ---------- | ----------- | ----------- | | bcftools | 1.22 | 1.23.1 | | fastp | 1.0.1 | 1.3.6 | | htslib | 1.22.1 | 1.24 | | minimap2 | 2.29 | 2.30 | | mosdepth | 0.3.11 | 0.3.14 | | multiqc | 1.34 | 1.35 | | picard | 3.4.0 | 3.5.0 | | prokka | 1.14.6 | 1.15.6 | | samtools | 1.22.1 | 1.24 | | snpeff | 5.4.0a | 5.4.0c | | vsearch | 2.21.1 | 2.31.0 | Parameters | Old parameter | New parameter | | ------------- | --------------------------- | | | --keep_unmapped | | | --normalise_reads | | | --arguments_bbnorm | | | --annotation_metadata | | | --use_host_filtered_reads | NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present.