mtb_mono_inh nextflow pipeline

A pipeline for analysing Mycobacterium tuberculosis samples.

Minimal requirements (for local execution)

• Nextflow VERSION > 21.04
• Java >= 8
• Docker

Pipeline workflow

Quick start

Local execution

1. Install nextflow

   Please refer to Nextflow page on github for more info.

2. Run it!

	nextflow run https://github.com/bioinformatics-lab/mtb_mono_inh_nf -params-file YOUR_PARAMS_FILE

$YOUR_PARAMS_FILE = file path, please refer to params/params.yml as a template to create your own params file

Configuration Profiles.

You can use diferent profiles for this pipeline, based on the computation enviroment at your disposal contained within conffolder.

Note: Update conf/profile with your own configs.

Tower execution

This Pipeline can be launched on Tower, please refer to Tower launch documentation for step-by-step execution tutorial.

When launching from Tower, please update and use the params.yml file contents.

Mock execution using stub-run

This project has the -stub-run feature, that can be used for testing propouse, it can be used on Tower with the Advanced settings on launch. You can also test it locally, using the following command:

cd data/mock_data/ && bash generate_mock_files.sh

nextflow run main.nf \
		 -profile conf/stub.config \
		 -stub-run