This patch release fixes an issue with Clair3 not producing variant calls for some regions due to full-alignment not being triggered. This issue was resolved by adding --var_pct_phasing=1, --var_pct_full=1 and --ref_pct_full=1 to the Clair3 command line. Changes fix: Added --var_pct_phasing=1, --var_pct_full=1 and --ref_pct_full=1 to Clair3 command line to ensure full-alignment is triggered for all reads to avoid missing variant calls in some regions. fix: Added stageAs: "input*/*" to CAT_NANOPORE_FASTQ process input channels to ensure that input files are not concatenated with themselves in an infinite loop until disk space is exhausted in rare cases. feat: Don't save NCBI Influenza reference sequences, metadata CSV and BLAST DB to the output directory by default. Added --save_ncbi_db and --save_blastdb workflow params to save these files to the output directory if desired. docs: Updated README.md to mention Apptainer. Updated usage.md to describe new workflow params. Updated output.md to better describe BLAST subtyping results. What's Changed Fix Clair3 sometimes missing variants by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/96 Release 3.6.1 by @peterk87 in https://github.com/CFIA-NCFAD/nf-flu/pull/97 Full Changelog: https://github.com/CFIA-NCFAD/nf-flu/compare/3.6.0...3.6.1