HLA-typing

Introduction

The pipeline does Human Leukocyte Antigen (HLA) typing using HLA-VBSEQ from high-throughput sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker and singularity containers making installation trivial and results highly reproducible.

Installation

1. Nextflow
2. Docker
3. Singularity

Running the pipeline

The pipeline does not require installation as NextFlow will automatically fetch it from GitHub.

Test data

To execute the pipeline on test dataset run:

```bash
nextflow run nanjalaruth/HLA-typing -profile test,singularity -r main --reference_genome "path to the human reference genome <hg19>" -resume
```

Own data

Start running your own analysis either by using flags as shown below:

```bash
nextflow run nanjalaruth/HLA-typing -profile singularity -resume --input "*_R{1,2}.fastq.gz" --reference_genome "path to the human reference genome <hg19>"  
```

or run your own analysis by modifying the conf/test.config file to suit the path to your data location and then run the command as below:

```
nextflow run nanjalaruth/HLA-typing -profile singularity -c <path to your edited config file> -resume
```

To run the updated version of this pipeline, run:

```bash
nextflow pull nanjalaruth/HLA-typing
```

Arguments

Required Arguments

Argument	Usage	Description
-profile	<base,slurm>	Configuration profile to use.
--input	</project/*_{R1,R2}*.fastq>	Directory pattern for fastq files.
--reference_genome	<hg19>	Path to the reference genome to which the samples will be mapped
--hla_ref	<'hla_ref.fasta'>	Path to the hla reference genome
--hla_txt_file	<Allele_v2.txt>	Path to the hla allele text file
-r	<revision>	Pipeline revision
--singleEnd		Specifies that the input files are not paired reads (default is paired-end).

Support

I track open tasks using github's issues