CFIA-NCFAD/nf-flu: 3.8.0

This release adds the --platform assemblies mode for analysis of FASTA sequences along with --input /path/to/fasta-dir/ to specify the directory containing the FASTA sequences.

Changes

• feat: analysis of previously assembled IAV FASTA sequences with the addition of a new analysis mode via --platform assemblies. Use along with --input /path/to/fasta-dir/ to specify the directory containing the FASTA sequences.
• fix: bin/cleavage_site.py short cleavage site index access error (#106)
• fix: cleavage_site.nf version output issue (#105)
• fix: low abundance indels appearing in consensus sequences despite major/minor allele frequency thresholds. Explicitly excluding non-SNP variants below the major allele fraction prior to consensus sequence generation with Bcftools consensus.
• fix: subtyping report issue with some poor quality IBV sequences (#107)
• dev: add nf-test for VCF filtering and consensus sequence generation from VCF with low AF indels.
• dev: replaced vcf_filter_frameshift.py with Bcftools filter commands.

What's Changed

• Add assemblies analysis mode by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/108
• Release 3.8.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/109

Full Changelog: https://github.com/CFIA-NCFAD/nf-flu/compare/3.7.0...3.8.0