The RIGHT Workflow

This is an ALL Fusion calling pipeline that uses Nextflow (DSL2).

Installation

Clone the repository to your system:

$ git clone https://github.com/ashleethomson/The-RIGHT-Workflow.git

Reference libraries and genomes

The GRCh37 reference genome and annotation was used for "Reproducible bioinformatics analysis workflows for detecting IGH gene fusions in B-cell acute lymphoblastic leukaemia patients". To replicate the results found in this paper, please use this version of the genome as well.

Reference libraries for each algorithm will need to be downloaded from their respective sources for this pipeline, as seen in the nextflow.config file, and a STAR Index needs to be created. You will have to install STAR to create the Index. STAR version 2.7.9a was used in the manuscript.

The STAR Index used was created using the following parameters:

STAR \
    --runMode genomeGenerate \
    --runThreadN 16 \
    --genomeDir star-2.7.9a-75bp \
    --genomeFastaFiles GRCh37.fa \
    --sjdbGTFfile ref-transcripts.gtf \
    --sjdbOverhang 74

Usage

1. Create a Sample-sheet

Create a CSV file with the following structure:

path,group,sample,filename,R1,R2
<path>,GROUP,TEST-0001,TEST-0001-XT,TEST-0001-XT_1.fastq.gz,TEST-0001-XT_2.fastq.gz

The columns are as follows:

path = Path to parent directory of Fastq files
group = Age group that sample belongs to e.g. GROUP
sample = Sample identifier e.g. TEST-0001
filename = Fastq file basename e.g. TEST-0001-XT
R1/R2 = Fastq filename (e.g TEST-0001-XT_1.fastq.gz)

2. Run the Pipeline

Use the following command to run the pipeline:

nextflow run \
    main.nf \
    -profile slurm,conda \
    -N email@email.com \
    --outdir ./outdir \
    --samplesheet <path>/test.csv \
    --email email@gmail.com \