Customizing BGCFlow config for analyzing fungal genomes

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How can I run BGCFlow for fungal genomes using a custom configuration?

Objectives

• Understand how to customize BGCFlow configuration for fungal genomes

• Learn how to run BGCFlow with a specific configuration for fungal genome analysis

Pre-requisite

• Activate the BGCFlow conda environment and make sure you have a clone of BGCFlow installed locally (see Part 1 - Introduction)

cd <your BGCFlow path>
git checkout dev-0.9.0-1
conda activate bgcflow

• Make sure to have the bgcflow_wrapper version 0.3.5 or above:

bgcflow --version
bgcflow_wrapper, version 0.3.5

Set up Fungi Project Configuration

• Inside the config folder, create a new project folder named fungi, the final project configuration will look like this:

config/
├── fungi
│   ├── project_config.yaml # BGCFlow project config
│   └── samples.csv # a csv files listing all your samples
└── config.yaml # BGCFlow global config

• Create the project_config.yaml and edit the contain to have this values:

name: Fungi
pep_version: 2.1.0
description: "Example of a fungi project."
input_folder: "."
input_type: "gbk" # BGCFlow does not have annotation tools for eukaryotes, so we will use the genbank from NCBI
sample_table: samples.csv

#### RULE CONFIGURATION ####
# rules: set value to TRUE if you want to run the analysis or FALSE if you don't
rules:
  seqfu: TRUE
  mash: TRUE
  fastani: FALSE
  checkm: FALSE
  gtdbtk: FALSE
  prokka-gbk: FALSE
  antismash: TRUE
  query-bigslice: TRUE
  bigscape: TRUE
  bigslice: TRUE
  automlst-wrapper: FALSE
  arts: FALSE
  roary: FALSE
  eggnog: TRUE
  eggnog-roary: FALSE
  deeptfactor: FALSE
  deeptfactor-roary: FALSE
  cblaster-genome: TRUE
  cblaster-bgc: TRUE

• Please note that some tools are not designed for for analysing fungal genomes.
• Create or edit samples.csv to have this values:

genome_id,source,organism,genus,species,strain,closest_placement_reference,input_file
GCA_014117465.1,ncbi,,,,,,
GCA_014784225.2,ncbi,,,,,,
GCA_030515275.1,ncbi,,,,,,
GCA_014117485.1,ncbi,,,,,,

Update the global configuration

• Now that we have our project ready, we need to update the global configuration so it is registered as one of the BGCFlow project to run
• Edit the config/config.yaml file to include only the fungal project to run:

# This file should contain everything to configure the workflow on a global scale.

#### PROJECT INFORMATION ####
# This section control your project configuration.
# Each project are separated by "-".
# A project can be defined as (1) a yaml object or (2) a Portable Encapsulated Project (PEP) file.
# (1) To define project as a yaml object, it must contain the variable "name" and "samples".
#   - name : name of your project
#   - samples : a csv file containing a list of genome ids for analysis with multiple sources mentioned. Genome ids must be unique.
#   - rules: a yaml file containing project rule configurations. This will override global rule configuration.
#   - prokka-db (optional): list of the custom accessions to use as prokka reference database.
#   - gtdb-tax (optional): output summary file of GTDB-tk with "user_genome" and "classification" as the two minimum columns
# (2) To define project using PEP file, only variable "name" should be given that points to the location of the PEP yaml file.
#   - pep: path to PEP .yaml file. See project example_pep for details.
# PS: the variable pep and name is an alias

projects:
# Project 2 (PEP file)
  - pep: config/fungi/project_config.yaml

bgc_projects:
  - pep: config/lanthipeptide_lactobacillus/project_config.yaml
...

Running the main BGCFlow pipeline

• Run the workflow by changing the config by:

snakemake --use-conda -c 8 --config "taxonomic_mode=fungi"

Key Points

• BGCFlow can be customized for analyzing fungal genomes using specific configurations

• Running BGCFlow with these configurations allows for targeted analysis of fungal genomes