nf-HAVoC is a bioinformatic pipeline designed to provide an accessible tool for constructing consensus sequences from SARS-CoV-2 FASTQ files and identifying the variants they belong to. The pipeline is an implementation of HAVoC (DOI: https://doi.org/10.1186/s12859-021-04294-2) and built on Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.

nf-HAVoC can be run to analyze FASTQ files within a directory/

The target directory must contain matching FASTQ files for forward (R1) and reverse (R2) reads, which can be either gzipped (*.fastq.gz) or uncompressed (*.fastq).

The following options can be changed as commandline options depending on your preferences:

* By default.

Only one tool can be utilized per option.

1. Install Nextflow (>=20.10.0)

2. Install any of Docker

3. Download test data and adapter and reference files

4. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run microsoft/nf-HAVoC -profile local --nextera 'path/to/NexteraPE-PE.fa' --ref path/to/ref.fa' --reads 'path/to/fastq/*R{1,2}*fastq.gz' =

5. Start running your own analysis on Azure.

Azure Batch Setup

Please refer to the Nextflow documentation which describe how to setup the Azure Batch environment.

```console
 nextflow run microsoft/nf-HAVoC -profile azure --nextera 'az://coantiner/NexteraPE-PE.fa' --ref 'az://container/ref.fa' --reads 'az://container/*R{1,2}*fastq.gz' -w 'az://conatiner/work'
```

* Azure speicifcs can be changed in the config locally or provided as commandline options*

These scripts were originally found Original Code. For more information visit Webpage Helsinki university Analyzer for Variants of Concern.

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