nf-iav-illumina 2.0.1 - 2021-06-15

Patch release to fix issue #5; added check that IRMA amended_consensus/ exists before concatenation of consensus FASTA files.

nf-iav-illumina 2.0.0 - 2021-06-10

⚠️ Major enhancements

• Samplesheet input (--input samplesheet.csv) replaces path to reads (--reads "reads/*_R{1,2}_*.fastq.gz"). Sample sheet can be tab-delimited (TSV) or CSV and must have a header line and 3 columns (sample name, FASTQ path/URL to forward reads, FASTQ path/URL to reverse reads).
• Pipeline has been re-implemented in Nextflow DSL2
• All software containers are now exclusively obtained from Biocontainers
• Updated minimum Nextflow version to v21.04.0 (see nextflow#572)
• Add IRMA params
  • irma_module: IRMA module (default: FLU-utr)
  • keep_ref_deletions: set consensus sequence deletion by ambiguation (i.e. replace ref seq with Ns) (default: true)
• Add BLAST subtyping params:
  • pident_threshold: % identity threshold (default: 0.85)
  • min_aln_length: min alignment length (default: 50)
• Replace Azure Pipelines CI with GitHub Actions CI
• add nextflow_schema.json and nf-core helper Jar file and Groovy scripts for params validation, printing help
• Use nf-core modules where possible
• Use nf-core module style for all processes
• Added usage and output docs
• Updated README

Parameters

Old parameter	New parameter
--reads	--input
	--irma_module
	--keep_ref_deletions
	--pident_threshold
	--min_aln_length
	--ncbi_influenza_fasta
	--ncbi_influenza_metadata
	--slurm_queue_size
	--publish_dir_mode
	--validate_params
	--enable_conda
	--singularity_pull_docker_container
	--show_hidden_params
	--schema_ignore_params

• NB: Parameter has been updated if both old and new parameter information is present.
• NB: Parameter has been added if just the new parameter information is present.
• NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
blast	2.9.0	2.10.0
irma	0.6.7	1.2.1
python	3.7.3	3.9.0

• NB: Dependency has been updated if both old and new version information is present.
• NB: Dependency has been added if just the new version information is present.
• NB: Dependency has been removed if new version information isn't present.