bahia-analysis nextflow pipeline

a pipeline for assemblying, anotating Mycobacterium Tuberculosis genomes and function prediction of antibiotic resistance that takes sra ids and handles the fastqs as inputs. it also integrates rd analyzer as a tool.

Requirements for local launch:

Nextflow VERSION > 20.11
Java 8
Docker

Pipeline workflow

This is the complete workflow of this pipeline.

Quick start

Local execution

Install nextflow

Please refer to Nextflow page on github for more info.
Run it!

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

$YOUR_PARAMS_FILE = FILE NAME, replace for your params file location, please refere to params_stardard.yml as template.

Configuration Profiles.

You can use diferent profiles for this pipeline, based on the computation enviroment at your disposal. Here are the Avaliable Profiles:

aws
gls
azureBatch
awsBatch

Note: Update conf/profile with your own credentials

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.

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:

bash data/mock_data/generate_mock_data.sh
nextflow run main.nf \
		 -params-file params/stub_params.yaml \
		 -stub-run

NOTE

Problematic samples:

ERR1035303
ERR1035365

emilyncosta/CPqGMFiocruzBA_MTB_MDR-XDR_nf