General schematic of the steps in the workflow

Contents

• Quick Start
• Introduction
• Installation
• Usage
• Parameters
  • Required parameters
  • Additonal parameters
• Resource Managers
• Output
• Troubleshooting
• Contributions and Support
• Citations

Quick Start: Test

Run the built-in test set to confirm all parts are working as-expected. It will also download all dependencies to make subsequent runs much faster.

Pull workflow from GitHub

nextflow pull bacterial-genomics/wf-assembly-snps -r main

Run test workflow

nextflow run \
  bacterial-genomics/wf-assembly-snps \
  -r main \
  -profile docker,test \
  --outdir results

Quick Start: Run

Example command on FastAs in "new-fasta-dir" data using BLAST with singularity:

Run workflow

nextflow run \
  bacterial-genomics/wf-assembly-snps \
  -r main \
  -profile docker \
  --input new-fasta-dir \
  --outdir my-results \
  --snp_package parsnp

Introduction

This workflow performs average nucleotide identity on assembled and/or annotated files (FastA/Genbank).

Installation

• Nextflow >=22.04.03
• Docker or Singularity >=3.8.0
• Conda is currently unsupported

Usage

nextflow run main.nf \
  -profile docker \
  --input <input directory> \
  --ref <optional reference file> \
  --outdir <directory for results> \
  --snp_package <parsnp>

Please see the usage documentation for further information on using this workflow.

Parameters

Note the "--" long name arguments (e.g., --help, --input, --outdir) are generally specific to this workflow's options, whereas "-" long name options (e.g., -help, -latest, -profile) are general nextflow options.

These are the most pertinent options for this workflow:

Required parameters

  ============================================
        Input/Output
  ============================================
  --input                 Path to input data directory containing FastA/Genbank assemblies or samplesheet.
                          Recognized extensions are:  {fasta,fas,fna,fsa,fa} with optional gzip compression.

  --ref                   Path to reference file in FastA format.
                          Recognized extensions are:  {fasta,fas,fna,fsa,fa} with optional gzip compression. [Default: NaN]

  --outdir                The output directory where the results will be saved.


  ============================================
        Container platforms
  ============================================
  -profile singularity    Use Singularity images to run the workflow.
                          Will pull and convert Docker images from Dockerhub if not locally available.

  -profile docker         Use Docker images to run the workflow.
                          Will pull images from Dockerhub if not locally available.


  ============================================
        Optional alignment tools
  ============================================
  --snp_package           Specify what algorithm should be used to compare input files.
                          Recognized arguments are: parsnp. [Default: parsnp]

Additional parameters

View help menu of all workflow options:

nextflow run \
  bacterial-genomics/wf-assembly-snps \
  -r main \
  --help \
  --show_hidden_params

Resource Managers

The most well-tested and supported is a Univa Grid Engine (UGE) job scheduler with Singularity for dependency handling.

1. UGE/SGE
   • Additional tips for UGE processing are here.
2. No Scheduler
   • It has also been confirmed to work on desktop and laptop environments without a job scheduler using Docker with more tips here.

Output

Please see the output documentation for a table of all outputs created by this workflow.

Troubleshooting

Q: It failed, how do I find out what went wrong?

A: View file contents in the <outdir>/pipeline_info directory.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.