XBS-nf (compleX Bacterial Samples) is a pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research.

• Fine-grained control over resource allocation (CPU/Memory/Storage)
• Reliance of bioconda for installing packages for reproducibility
• Ease of use on a range of infrastructure (cloud/on-prem HPC clusters/ servers (or local machines))
• Resumability for failed processes
• Centralized locations for specifying analysis parameters and hardware requirements
  • XBS-nf parameters (default_parameters.config)
  • Hardware requirements (conf/standard.config)
  • Execution (software) requirements (conf/docker.config or conf/conda.config)
• A GVCF reference dataset for ~600 samples

For the usage and tutorials please refer the XBS-nf website

• git and git-lfs

NOTE: Without the git-lfs tool the optional bundled wouldn't be downloaded correctly.

• Java-11 or Java-17 (preferred)

NOTE: The java version should NOT be an internal jdk release! You can check the release via java -version

• Download Nextflow

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

• Make Nextflow executable

$ chmod +x nextflow

• Add nextflow to your path (perhaps /usr/local/bin/)

$ mv nextflow /usr/local/bin

• Sanity check for nextflow installation

$ nextflow info

  Version: 22.04.5 build 5708
  Created: 15-07-2022 16:09 UTC (18:09 SAST)
  System: Mac OS X 10.15.6
  Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1+1-LTS
  Encoding: UTF-8 (UTF-8)

NOTE: The conda environments are expected by the conda_local profile to be created within xbs-nf/conda_envs directory

• Clone the pipeline locally and cd into it

$ git clone https://github.com/TORCH-Consortium/xbs-nf

$ cd xbs-nf

• cd in the conda_envs folder and execute the following commands

$ conda env create -p xbs-nf-env-1 --file xbs-nf-env-1.yml

$ conda env create -p xbs-nf-env-2 --file xbs-nf-env-2.yml

TIP: For faster installation process, please download mamba tool and replace conda with mamba in the above commands.

• Customize the pipeline and process level settings in the default_params file

• From inside the xbs-nf folder, invoke the pipeline

$ nextflow run main.nf -profile conda

• use the -resume flag to continue from previously generated output files, rather than starting from scratch.

$ nextflow run main.nf -profile conda -resume

Contributions are warmly accepted!

Please refer the LICENSE file.