Geniac-demo pipeline

• Introduction
• Quick start
• Geniac documentation and useful resources
• Pipeline documentation
• Acknowledgements
• Release notes
• Citation

Introduction

This is a demo pipeline with the best practises for the development of bioinformatics analysis pipelines with Nextflow and geniac (Automatic Configuration GENerator and Installer for nextflow pipelines). It runs within ~20 seconds a very simple bioinformatics pipeline inspired from the analysis of high-throuphput-sequencing data. The best practises proposed by geniac can be applied to any analysis workflow in data science.

This pipeline illustrates how geniac can automatically build: * Nextflow profiles configuration files * Singularity / Docker recipes and containers * Run the pipeline with the different Nextflow profiles

Quick start

Prerequisites

• git (>= 2.0) [required]
• cmake (>= 3.0) [required]
• Nextflow (>= 21.10.6) [required]
• Singularity (>= 3.8.5) [optional]
• Docker (>= 18.0) [optional]

Install conda: bash wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh

Install the geniac conda environment

```bash

Create the geniac conda environment

export GENIACCONDA="https://raw.githubusercontent.com/bioinfo-pf-curie/geniac/release/environment.yml" wget ${GENIACCONDA} conda env create -f environment.yml conda activate geniac pip install geniac ```

Check the code, install and run the pipeline with the multiconda profile

```bash export WORKDIR="${HOME}/tmp/myPipeline" export INSTALLDIR="${WORKDIR}/install" export GITURL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

Initialization of a working directory

with the src and build folders

geniac init -w ${WORKDIR} ${GITURL} cd ${WORK_DIR}

Check the code

geniac lint

Install the pipeline

geniac install . ${INSTALL_DIR}

Test the pipeline with the multiconda profile

geniac test multiconda ```

Check the code, install and run the pipeline with the singularity profile

Note that you need sudo privilege to build the singularity images.

```bash export WORKDIR="${HOME}/tmp/myPipeline" export INSTALLDIR="${WORKDIR}/install" export GITURL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

Initialization of a working directory

with the src and build folders

geniac init -w ${WORKDIR} ${GITURL} cd ${WORK_DIR}

Install the pipeline with the singularity images

geniac install . ${INSTALL_DIR} -m singularity sudo chown -R $(id -gn):$(id -gn) build

Test the pipeline with the singularity profile

geniac test singularity

Test the pipeline with the singularity and cluster profiles

geniac test singularity --check-cluster ```

Advanced users

Note that the geniac command line interface provides a wrapper to git, cmake and make commands. Advanced users familiar with these commands can run the following (see geniac documentation for more details):

```bash export WORKDIR="${HOME}/tmp/myPipeline" export SRCDIR="${WORKDIR}/src" export INSTALLDIR="${WORKDIR}/install" export BUILDDIR="${WORKDIR}/build" export GITURL="https://github.com/bioinfo-pf-curie/geniac-demo.git"

mkdir -p ${INSTALLDIR} ${BUILDDIR}

clone the repository

the option --recursive is needed if you use geniac as a submodule

the option --remote-submodules will pull the last geniac version

using the release branch from https://github.com/bioinfo-pf-curie/geniac

git clone --remote-submodules --recursive ${GITURL} ${SRCDIR} cd ${BUILD_DIR}

configure the pipeline

cmake ${SRCDIR}/geniac -DCMAKEINSTALLPREFIX=${INSTALLDIR}

build the files needed by the pipeline

make

install the pipeline

make install

run the pipeline

make test_multiconda ```

Pipeline documentation

The geniac-demo pipeline is a very simple bioinformatics pipeline inspired from the analysis of high-throuphput-sequencing data. More information are available here:

1. Running the pipeline
2. Nextflow profiles
3. Outputs

Geniac documentation and useful resources

• The geniac documentation provides a set of best practises to implement Nextflow pipelines.
• The geniac source code provides the set of utilities.
• The geniac demo provides a toy pipeline to test and practise Geniac.
• The geniac demo DSL2 provides a toy pipeline to test and practise Geniac.
• The geniac template provides a pipeline template to start a new pipeline.

Acknowledgements

• Institut Curie
• Centre national de la recherche scientifique
• This project has received funding from the European Union’s Horizon 2020 research and innovation programme and the Canadian Institutes of Health Research under the grant agreement No 825835 in the framework on the European-Canadian Cancer Network.

Citation

Allain F, Roméjon J, La Rosa P et al. Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines. Open Research Europe 2021, 1:76.