Installation

Prerequisites

To run this pipeline, you need the following prerequisites:

• Nextflow

• Python

• FastQC

• MultiQC

• Trimmmomatic

• Chopper

• BWA-MEM2

• minimap2

• GATK

• Medaka

• bcftools

• samtools

• FHIR validator

Setup

1. Clone the repository for local installation:

   git clone https://github.com/oucru-id/tb-to-fhir-full.git
   cd tb-mutation-pipeline
   

2. Install Nextflow:

   curl -s https://get.nextflow.io | bash
   

3. Testing the Nextflow install:

   nextflow -v
   

Usage

Get Access Token (FHIR Upload)

python scripts/get_access_token.py

Basic Run

nextflow run main.nf

Run with FHIR Upload

Get the access token first before running with upload.

nextflow run main.nf \
  --fhir_server_url "https://<BASE_URL>/fhir"