IAEA_wgsbac-docker

Docker image for the WGSBAC pipeline for Salmonella and Brucella in the context of IAEA-GenPat joint project.

Index

• Overview
• About the Project
• Disclaimer
• Features
• Requirements
• Installation
• How to run
• Acknowledgement
• Final Notes

Overview

This repository hosts the Dockerfile, developed by GenPat's bioinformatics team, and necessary dependencies (yml and envs.zip) to build the Docker for the WGSBAC pipeline (https://gitlab.com/FLI_Bioinfo/WGSBAC) by Jörg Linde (@joerg.linde) and Mostafa Abdel-Glil (@Mostafa.Abdel-Glil).

• Version: 1.0.0
• Author: GenPat
• Contact: [email protected]

About the Project

In the context of the 2024-2025 IAEA-GenPat joint project, the GenPat platform ensured interoperability with the Galaxy platform, by adapting and transfering bioinformatics workflows. This repository hosts the development results of the migration and adaptation of the bacterial workflows (for Brucella and Salmonella), from the contact of the Friedrich-Loeffler-Institut (Jörg Linde: [email protected]).

The developed dockerized version of the original software (wgsbac.pl) was used for deployment of the analyses for the 2 organisms of interest on the GenPat platform.

• GenPat platform: https://genpat.izs.it
• Galaxy platform: https://usegalaxy.org

Disclaimer

The code in this repo has been developed uniquely for the needs of the GenPat platform, and published here to share it with the open source community and the authors, and in accordance with the original authors' MIT license.

Only commands and tools of interest were tested, and some adaptations were added to allow integration of the pipeline into the GenPat platform, for IAEA users.

As such, the Dockerfile's code in this repository is provided "as is", without warranty of any kind, express or implied, including but not limited to fitness for a particular purpose.

Features

The dockerized WGSBAC pipeline runs a suite of tools that can be subdivided into:

• Reads Quality Check (QC) and trimming
• Sequence reconstruction
• Assembly QC and contamination check
• Genome annotation
• Typing

The list of analyses run for Brucella and Salmonella species and the tools used are available on the official WGSBAC software's GitLab page: https://gitlab.com/FLI_Bioinfo/WGSBAC#modules. The list of analyses available in this dockerized version are listed in the tables below.

• For execution on Brucella samples:

Analysis	Tool/DB
contamination check	confindr
coverage calculation	custom script
trimming and QC	fastp
raw reads quality check	fastqc
contamination check	kraken2
Multi Lucus Sequence Typing	mlst
QC	multiQC, fastQC
plasmid identification	plasmidfinder/platon
assembly QC	Quast
de novo assembly	Shovill
variant calling	Snippy
species identification	Sourmash
Anti-Micorbial Resistance (AMR) detection	AMRFinderPlus

• For execution on Salmonella samples:

Analysis	Tool/DB
contamination check	confindr
coverage calculation	custom script
trimming and QC	fastp
raw reads quality check	fastqc
contamination check	kraken2
Multi Lucus Sequence Typing	mlst
QC	multiQC, fastQC
plasmid identification	plasmidfinder/platon
assembly QC	Quast
de novo assembly	Shovill
variant calling	Snippy
species identification	Sourmash
Anti-Micorbial Resistance (AMR) detection	AMRFinderPlus
virulence genes identification	SPI
Salmonella serotype prediction	seqSero
Salmonella serovar prediction	sistr

Requirements

• wgsbac_env_20250210.yml (configuration file of the main environment);
• envs.zip (archive of configuration files for wgsbac.pl's tools);
• Docker and its relevant dependencies;
• access to kraken2 and confindr databases (they need to be provided as directories on the host system);
• git (optional, if cloning this repo).

Dependencies for wgsbac.pl (https://gitlab.com/FLI_Bioinfo/WGSBAC#install-wgsbac) are managed inside the container and dealt with through the wgsbac_env_20250210.yml and envs.zip files, during build.

Installation

• Clone repository:

# clone repo
git clone https://github.com/genpat-it/iaea_wgsbac-docker.git

# move into repository directory
cd iaea_wgsbac-docker/
## check contents
ls
Dockerfile  envs.zip  LICENSE  README.md  wgsbac_env_20250210.yml

• Build Docker:

# docker build command
docker build -t wgsbac:1.0 .

NOTE: the docker has steps to clone some necessary databases and the wgsbac repository in the container's context. This will take some time to execute and also requires ~11GB of disk space for the final image.

How to run

After building, you can run the container with:

docker run --rm -it -v $(pwd):/wd wgsbac:1.0

To run the whole pipeline, provide the desired wgsbac command after the docker run call. Please follow instructions on WGSABAC's official GitLab to build the desired command for the species of interest. Below you'll find examples of full analysis for the 2 supported species:

• for Brucella:

docker run --rm -it -v $(pwd):/wd wgsbac:1.0 wgsbac.pl --table metadata_brucella.tsv --results test_brucella --kraken minikraken_8GB_20200312 --mlst brucella --virulence --conf confindr --snippy --plasmid --cpus 100 --run

• for Salmonella:

docker run --rm -it -v $(pwd):/wd wgsbac:1.0 wgsbac.pl --table metadata_salmonella.tsv --results test_salmonella --kraken minikraken_8GB_20200312 --mlst senterica --seqsero --sistr --amr --amrorganism Salmonella --virulence --spi --conf confindr --snippy --plasmid --cpus 100 --run

NOTE 1: kraken2 and confindr databases are not cooked inside the container: ensure you have access to them (especially confinder's full version) because they are needed to run the most basic analysis possible with wgsbac.pl.

NOTE 2: remember to map necessary directories with Docker's -v option: if external databases (confindr and kraken2) are not in the working directory, ensure the container can read their directories and that correct paths are provided.

Final Notes

• The following 2 files are necessary because of how the original WGSBAC software needs to be installed (https://gitlab.com/FLI_Bioinfo/WGSBAC#install-wgsbac) and because of how it runs different tools:
  • wgsbac_env_20250210.yml is a Conda configuration file, needed to automatically create the main wgsbac Conda environment in the Docker;
  • envs.zip is an archive containing Conda configuration files for each tool used by wgsbac.pl.
• During build, the Docker will git clone the WGSBAC pipeline from the official GitLab page and it will update the following databases, cooked in the container:
  • bakta_db_light_250210
  • amrfinderplus-db
  • Platon
  • SPI (spis_ibiz_database)
• kraken2 and confindr databases are necessary for the pipeline execution, but are not cooked in the Docker container, so they need to be mapped with the -v flag;
• The custom Rscript table2itol.R is disabled through commands run in the Dockerfile. If you wish to turn it on again, just delete or comment lines 46 and 47 of the Dockerfile;
• Only analysis relevant for this project (i.e. for Salmonella and Brucella) will work, since those are the only ones that have been set up and tested:
• All commands passed to the container will be executed in the created Conda environment (wgsbac).

Acknowledgements

This is not an official Docker release of the WGSBAC pipeline.

GenPat's bioinformatics group has no control nor rights over the WGSBAC sofware, except for the permissions granted by its authors through the provided license. The Docker for such pre-existing software is provided with WGSBAC's original license.

The group sincerely thanks the author Jörg Linde for their kind support during development of this piece of software.