TBPipe

TB analysis pipeline by Arnold Bainomugisa/QH.

Adapted to NextFlow/additional development by Dr. Brian Forde and Thom Cuddihy

Prerequisites

• nextflow <= 22.10.6 (needs to support WSL1)
• singularity (sylabs) >= 3.7.1

Setup

Clone repo Make a copy/symlink of nextflow.config.slurm or nextflow.config.slurm (as appropriate) to nextflow.config

Some changes may be appropriate depending on your system.

Usage

Copy nextflow.config.user to project directory as nextflow.config and edit as needed.

Run pipeline with:

nextflow run /my/cloned/repo/tbpipe/main.nf

You can use --parameter e.g., but I recommend using a project level nextflow.config file for auditing purposes.

Useful

You can resume a job (from an error e.g.) with:

nextflow run /my/cloned/repo/tbpipe/main.nf -resume

Images

Pre-built singularity images can be downloading from here: TBA

Building

See docker/build_add.sh for overview. Change as needed. You will also need to download the TBPipe database folder and place it in the root of this repository. You can find it here: TBA

Kraken2 DB

TBPipe by default will attempt to use a Kraken2 database located at /dev/shm/Kraken2 on the compute node/local host.

Pre-built Kraken databases can be downloaded from here.

If not using /dev/shm (RAM disk), be sure to change nextflow.config as appropriate.