CFIA-NCFAD/nf-flu: 3.9.0

This minor release adds Nextclade analysis of assembled Influenza genome sequences against 30 Nextclade Influenza-related datasets by default and updates the Influenza sequences used by nf-flu (downloaded from NCBI 2025-04-04; 809,739 unique sequences and metadata).

The specific Nextclade datasets and optionally versions (tags) can be configured with a headerless CSV file. Nextclade results are aggregrated across samples and datasets and filtered for positive results into a single Nextclade TSV (tab-separated values) report with additional fields capturing sample, dataset name and dataset version/tag information as well as Nextclade and Nextclade dataset specific results.

Changes

• update: Influenza sequences and metadata from NCBI (2025-04-04). 809,739 non-redundant, unique sequences were retrieved along with their metadata. Added documentation for how to update Influenza sequences for use with nf-flu (see docs/update_seqs_db.md)
• feat: added Nextclade (v3.12.0) analysis subworkflow against 30 Influenza-related Nextclade datasets with a convenient aggregation and summarization of useful results into a single Nextclade TSV report.
• update: GenoFLU 1.05 -> 1.06 (#112)

What's Changed

• Add Nextclade, update seqs DB and GenoFLU by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/113
• Release 3.9.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/114

Full Changelog: https://github.com/CFIA-NCFAD/nf-flu/compare/3.8.1...3.9.0