Update docs

CHANGELOG.md

@@ -3,6 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.3.0](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.0)] - 2023-07-11
+
+This release migrates to more recently updated Influenza virus sequences since the last update for the [NCBI Influenza DB FTP data](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/) was in 2020-10-13. By default, all Orthomyxoviridae virus sequences were parsed from the daily updated NCBI Viruses [`AllNucleotide.fa`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNucleotide/) and [`AllNuclMetadata.csv.gz`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/AllNuclMetadata.csv.gz) and uploaded to [Figshare](https://figshare.com/articles/dataset/2023-06-14_-_NCBI_Viruses_-_Orthomyxoviridae/23608782) as Zstd compressed files. nf-flu no longer uses the [influenza.fna.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz) and [genomeset.dat.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/genomeset.dat.gz) files for Influenza sequences and metadata, respectively.
+
+### Fixes
+
+* More up-to-date Influenza sequences database used by default (#24)
+
 ## [[3.2.1](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.2.1)] - 2023-07-07
 
 ### Fixes

README.md

@@ -17,13 +17,14 @@ After reference sequence selection, the pipeline performs read mapping to each r
 
 ## Pipeline summary
 
-1. Download latest [NCBI Influenza DB][] sequences and metadata (or use user-specified files)
-2. Merge reads of re-sequenced samples ([`cat`](http://www.linfo.org/cat.html)) (if needed)
+1. Download latest [NCBI Orthomyxoviridae sequences](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=11308&lvl=3&keep=1&srchmode=1&unlock) and metadata (parsed from [NCBI Viruses FTP data](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNucleotide/)).
+2. Merge reads of re-sequenced samples ([`cat`](http://www.linfo.org/cat.html)) (if needed).
 3. Assembly of Influenza gene segments with [IRMA][] using the built-in FLU module
-4. Nucleotide [BLAST][] search against [NCBI Influenza DB][]
-5. Automatically select top match references for segments
-6. H/N subtype prediction and Excel XLSX report generation based on BLAST results
-7. Perform Variant calling and genome assembly for all segments.
+4. Nucleotide [BLAST][] search against [NCBI Influenza DB][] sequences
+5. H/N subtype prediction and Excel XLSX report generation based on BLAST results.
+6. Automatically select top match reference sequences for segments
+7. Read mapping, variant calling and consensus sequence generation for each segment against top reference sequence based on BLAST results.
+8. MultiQC report generation.
 
 ## Quick Start
 

docs/output.md

@@ -78,7 +78,7 @@ The primary output from [IRMA][] are the consensus sequences for gene segments,
 
 </details>
 
-Nucleotide [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi) (`blastn`) is used to query [IRMA][] assembled gene segment sequences against the [NCBI Influenza DB][] sequences (and optionally, against user-specified sequences (`--ref_db`) to predict the H and N subtype of each sample if possible (i.e. if segments 4 (hemagglutinin) and/or 6 (neuraminidase) were assembled) and to determine the closest matching reference sequence for each segment for reference mapped assembly.
+Nucleotide [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi) (`blastn`) is used to query [IRMA][] assembled gene segment sequences against [Influenza sequences from NCBI](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNucleotide/) (and optionally, against user-specified sequences (`--ref_db`) to predict the H and N subtype of each sample if possible (i.e. if segments 4 (hemagglutinin) and/or 6 (neuraminidase) were assembled) and to determine the closest matching reference sequence for each segment for reference mapped assembly.
 
 ### Coverage Plots
 

docs/usage.md

@@ -261,17 +261,17 @@ Maximum of top blastn result reported
 
 - Optional
 - Type: string
-- Default: `https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz`
+- Default: `https://api.figshare.com/v2/file/download/41415330`
 
-Path/URL to NCBI Influenza DB sequences FASTA file.
+Path/URL to Zstandard compressed NCBI Influenza virus sequences FASTA file.
 
 #### `--ncbi_influenza_metadata`
 
 - Optional
 - Type: string
-- Default: `https://ftp.ncbi.nih.gov/genomes/INFLUENZA/genomeset.dat.gz`
+- Default: `https://api.figshare.com/v2/file/download/41415333`
 
-Path/URL to NCBI Influenza DB metadata file.
+Path/URL to Zstandard compressed NCBI Influenza virus sequences metadata CSV file.
 
 ### Generic options
 

nextflow.config

@@ -153,7 +153,7 @@ manifest {
  description = 'Influenza A virus genome assembly pipeline'
  homePage = 'https://github.com/CFIA-NCFAD/nf-flu'
  author = 'Peter Kruczkiewicz, Hai Nguyen'
- version = '3.2.1'
+ version = '3.3.0'
  nextflowVersion = '>=21.10'
  mainScript = 'main.nf'
  doi = '10.5281/zenodo.7011213'

nextflow_schema.json

@@ -213,14 +213,14 @@
  },
  "ncbi_influenza_fasta": {
  "type": "string",
- "default": "https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz",
- "description": "Path/URL to NCBI Influenza DB sequences FASTA file.",
+ "default": "https://api.figshare.com/v2/file/download/41415330",
+ "description": "Path/URL to Zstandard compressed NCBI Influenza virus sequences FASTA file.",
  "fa_icon": "fas fa-file-alt"
  },
  "ncbi_influenza_metadata": {
  "type": "string",
- "default": "https://ftp.ncbi.nih.gov/genomes/INFLUENZA/genomeset.dat.gz",
- "description": "Path/URL to NCBI Influenza DB metadata file.",
+ "default": "https://api.figshare.com/v2/file/download/41415333",
+ "description": "Path/URL to Zstandard compressed NCBI Influenza virus sequences metadata CSV file.",
  "fa_icon": "fas fa-file-csv"
  }
  },