Named after Grandeur Peak.

Image Credit: ryancornia Location: 40.707, -111.76, 8,299 ft (2,421 m) summit. Trail Info: https://utah.com/hiking/grandeur-peak

Grandeur is a species-agnostic sequencing analysis workflow developed by @erinyoung at the Utah Public Health Laboratory (UPHL). Built on Nextflow, the pipeline provides quality control (QC), de novo assembly, taxonomic profiling, and in silico serotyping for paired-end Illumina data.

While intended to augment the CDC's PHOENIX workflow, Grandeur also functions as a powerful standalone pipeline.

• Nextflow (>= 25.0.0)
• Apptainer/Singularity or Docker

# Execution with FASTQ reads (Singularity)
nextflow run UPHL-BioNGS/Grandeur -profile singularity --reads <path_to_fastqs>

# Execution with existing Assemblies (Docker)
nextflow run UPHL-BioNGS/Grandeur -profile docker --fastas <path_to_fastas>

# Execution of a full Phylogenetic Analysis
nextflow run UPHL-BioNGS/Grandeur -profile singularity --sample_sheet samples.csv --msa

Grandeur is modular and executes the following stages based on inputs and flags:

1. De Novo Alignment: Cleaning reads with fastp and assembling with SPAdes.
2. Taxonomic Profiling: Rapid identification via SKANI, Kraken2, Mash, and Sylph.
3. Quality Assessment: Assembly metrics via QUAST, CheckM2, and FastQC.
4. Subtyping: Organism-specific serotyping (e.g., Kleborate, SeqSero2, Legionella SBT).
5. Phylogenetic Analysis (Optional): Core genome alignment and Maximum Likelihood trees.

Detailed guides, FAQ, and process explanations are located in the Grandeur Wiki.

• Installation
• Usage Examples
• Phylogenetic Analysis
• Subworkflow Explanations

NF-CORE style docs can be found in docs

nextflow run UPHL-BioNGS/Grandeur --help

Running the workflow with --help should display a help message like the following.

 N E X T F L O W   ~  version 25.10.4

Launching `UPHL-BioNGS/Grandeur` [furious_bardeen] DSL2 - revision: 8a4591f1a0

Typical pipeline command:

  nextflow run UPHL-BioNGS/Grandeur -profile docker --sample_sheet samplesheet.csv --outdir grandeur

--help                [boolean, string] Show the help message for all top level parameters. When a parameter is given to `--help`, the full help message of that parameter will be printed.
--help_full           [boolean]         Show the help message for all non-hidden parameters.
--show_hidden         [boolean]         Show all hidden parameters in the help message. This needs to be used in combination with `--help` or `--help_full`.

Input/output options
  --sample_sheet      [string] csv with sample,read1,read2
  --fasta_list        [string] A sample sheet for fasta files
  --outdir            [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. [default: grandeur]

Reference files/paths
  --checkm2_db        [string] prepared checkm2 reference file
  --kraken2_db        [string] directory of kraken2 database
  --mash_db           [string] prepared mash reference msh file
  --sylph_db          [string] prepared sylph reference file
  --reference_genomes [string] list of genomes (in fasta format) for ANI references

workflow values
  --min_core_genes    [integer] minimum number of genes in core genome alignment for iqtree2 (default is 500) [default: 500]
  --min_core_per      [number]  minimum percentage number of core genes in core genome alignment for iqtree2 (default is 0.5 or 50%) [default: 0.5]

Subworkflow toggles
  --msa               [boolean] toggles whether or not phylogenetic analysis will be run on samples

 !! Hiding 27 param(s), use the `--show_hidden` parameter to show them !!
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Issues and problems should be submitted to the GitHub Issues page.

Grandeur wouldn't be possible without the following tools:

• nf-tools - for keeping the schema functional
• nf-docs - creation of nf-core style docs found in docs
• amrfinderplus - identification of genes associated with antimicrobial resistence
• bakta - gene prediction
• checkm2 - assembly QC
• datasets - downloads genomes from NCBI
• drprg - TB AMR predictions
• elgato - Legionella pneumophila Sequence Based Typing (SBT)
• emmtyper - Group A Strep "emm" typing
• enatools - download fastq files from the ENA
• fastp - cleaning reads
• fastqc - fastq file QC
• gotree - stats and visualization of newick files
• heatcluster - visualizes SNP matrix from SNP dists
• iqtree - phylogenetic tree creation - used after core genome alignment
• kaptive - Vibrio and Acinetobacter subtyping
• kleborate - Klebsiella and Escherichia serotyping
• kraken2 - contamination
• mash - species identifier
• mashtree - tree based on mash distances (not impacted by size of core genome)
• meningotype - Neisseria subtyping
• mlst - identification of MLST subtype
• multiqc - summarizes QC efforts
• mykrobe - Mycobacterium subtyping
• ngmaster - Neisseria subtyping
• panaroo - core genome alignment - optional (set with params.msa = true)
• pbptyper - Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
• plasmidfinder - MLST typing for plasmids
• prokka - gene annotation - used for core genome alignment
• quast - contig QC
• roary - core genome alignement - optional (set with params.msa = true)
• seqsero2 - Salmonella serotyping
• seqsero2S - Salmonella serotyping
• serotypefinder - E. coli serotyping
• shigapass - Shigella serotyping
• ska2 - sequencing comparison
• skani - ani comparison
• snp-dists - SNP matrix - used after core genome aligment
• spades - de novo alignment
• spestimator - species estimation
• sylph - taxonomic profiling

The expected tools are split into multiple processes. Each process has its own wiki page that we encourage users to view.