Skip to content

1. Usage

Jump to bottom
Jérémy Rousseau edited this page Jan 14, 2026 · 3 revisions

Table of contents

Introduction

The Nextflow process must run until the pipeline is completed, it is therefore advisable to run the pipeline in the background. Nextflow automatically handles job submission (SLURM, PBD, etc.), so the pipeline can be used on a computing cluster.

How to install the pipeline

Local installation

LAGOON-MCL uses Nextflow as workflow manager, and Singlularity as container manager. If you're using it on a cluster, Nextflow handles job submission (SLURM, PBS, etc.).

Check that Nextflow and Apptainer are installed on your system.

Install LAGOON-MCL

Retrieve the files available on the GitHub repository.

git clone https://github.com/jroussea/lagoon-mcl.git
cd lagoon-mcl

Download containers

The containers used by LAGOON-MCL are available at BioContainers.

  • Diamond (v2.1.10) \
  • MCL (v22.282) \
  • MMseqs2 (v15.6f452) \
  • SeqKit2 (v2.9.0) (used only to build Pfam and AlphaFold databases)

A LAGOON-MCL-specific container is available at Docker Hub. It contains Python (v3.12.6) as well as the modules pandas (v2.2.3), numpy (v2.2.2), python-igraph (v0.11.8), biopython (v1.85), seaborn (v0.13.2) and jinja2 (v3.1.5). For more information on the container, and to view the dockerfile, please consult the containers/lagoon-mcl/1.0.0 directory. Unlike the four previous containers, you need to build the Singularity container from the Docker image using the : apptainer build --fakeroot [apptainer container] [docker image].

# SeqKit2 v2.9.0
wget -O containers/seqkit/2.9.0/seqkit.sif https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0

# Diamond v2.1.10
wget -O containers/diamond/2.1.10/diamond.sif https://depot.galaxyproject.org/singularity/diamond:2.1.10--h43eeafb_2

# MCL v22.282
wget -O containers/mcl/22.282/mcl.sif https://depot.galaxyproject.org/singularity/mcl:22.282--pl5321h031d066_2

# MMseqs2 v15.6f452
wget -O containers/mmseqs2/15.6f452/mmseqs.sif https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_3

# LAGOON-MCL v1.0.0
apptainer build --fakeroot containers/lagoon-mcl/1.0.0/lagoon-mcl.sif docker://jroussea/lagoon-mcl:latest

Containers can be found in: containers/

Download and build databases

LAGOON-MCL uses the Pfam and AlphaFold Protein Structure Databases to obtain sequence information. 4. Databases détaille les méthodes utilisé pour télécharger les banques de données.

cd tool-kit/

# Download Alphafold Protein Database [mandatory]
./build_alpahfold_db.sh

# Dowload Pfam [optional]
./build_pfam_db.sh

Databases are available in the database/ folder.

Cluster configuration

If you are using LAGOON-MCL on a computing cluster, you will need to provide Nextflow with a configuration file specific to your system. Information on executors (SLURM, PBS, AWS, ...) can be found in the executor section of the Nextflow documentation. For some institutes, this file is already referenced in nf-core/configs. If this is the case, you can download the file and use it with -c path/to/your/institute/config/file/institute_file.config when executing the pipeline.

Running the pipeline

nextflow run main.nf -profile singularity -params-file params_test.yaml

The files params_test.yaml and params.yaml contain the various parameters used for running LAGOON-MCL.

For more information on running the pipeline, please see the 3. Tutorial.

Updating the pipeline

Retrieve the latest version of the pipeline from the GitHub repository.

cd lagoon-mcl/
git pull

Usage

All parameters are available here

Clone this wiki locally