CFIA-NCFAD/nf-flu v3.1.0

The workflow's name has been changed from nf-iav-illumina to nf-flu and the official repo for nf-flu will be CFIA-NCFAD/nf-flu going forward.

Version 3 is a major release adding a Nanopore influenza sequence analysis subworkflow using IRMA for initial assembly and BLAST against NCBI Influenza DB sequences and optionally, user-specified sequences to identify the top reference sequence for each segment for each sample. A standard read mapping/variant calling analysis is performed: for each sample, Nanopore reads are mapped separately against each gene segment reference sequence using Minimap2; variant calling of read alignments is performed using Clair3; depth-masked consensus sequence is generated using Bcftools. Consensus sequences are BLAST searched against NCBI Influenza (and user-specified sequences) to generate a BLAST summary report and H/N subtyping report. MultiQC is used to summarize results into an interactive HTML report.

NOTE: Read mapping/variant calling analysis has not been ported to the Illumina sequence analysis subworkflow.

3.1.0 changes

• Added back bin/fastq_dir_to_samplesheet.py for Illumina --input samplesheet creation from Illumina FASTQ reads directory
• Fixed issue #12. Nanopore sample sheet can specify a mix of single FASTQ files and/or directories containing FASTQ files. Different reads with the same sample name will be merged prior to analysis. FASTQs can be GZIP compressed and have the extensions: .fastq, .fq, .fastq.gz, .fq.gz. Updated CI tests to test for this flexible sample sheet handling.
• Switched to GitHub YAML form for bug report template from Markdown template.
• CI tests now output results/pipeline_info/ and .nextflow.log as artifacts for easier debugging of issues.