CFIA-NCFAD/nf-flu: 3.7.0

This minor release adds GenoFLU for H5 genotyping and HA cleavage site output with VADR annotations. This release also adds a script to classify HA cleavage sites based on mono-/multibasicity and low/high pathogenicity.

Changes

• feat: GenoFLU v1.05 for H5 genotyping.
• feat: Added --custom_flu_minfo option to specify custom flu.minfo for VADR. The default flu.minfo is the same as the VADR flu v1.6.3-2 model except that it includes cleavage site info. Feature table, GenBank and GFF files should now have a misc_feature for HA cleavage site info.
• feat: bin/cleavage_site.py to classify HA cleavage sites.
• feat: Added VADR subtype prediction into subtyping report. VADR subtype predictions are pulled from the output .mdl files.
• feat: Added subtyping report output directory containing CSV for each sheet in the Excel report.
• fix: MultiQC converts the general info table into a violin plot if there are more than 500 rows in the table by default. Added max_table_rows: 1000000 to multiqc_config.yaml to avoid this conversion in most cases.

What's Changed

• Add GenoFLU and HA cleavage site prediction by @cerdelyan in https://github.com/CFIA-NCFAD/nf-flu/pull/103
• Release 3.7.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/104

New Contributors

• @cerdelyan made their first contribution in https://github.com/CFIA-NCFAD/nf-flu/pull/103

Full Changelog: https://github.com/CFIA-NCFAD/nf-flu/compare/3.6.2...3.7.0