nextflow pipeline

This repository is a template and a library repository to help you build nextflow pipeline.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

To run nextflow on you computer you need to have java (>= 1.8) installed.

java --version

To be able to easily test tools already implemented for nextflow on your computer (src/nf_modules/ to see their list). You need to have docker installed.

docker run hello-world

Installing

To install nextflow on you computer simply run the following command:

src/install_nextflow.sh

Then to initialise a given tools run the following command:

src/nf_modules/<tool_name>/<tool_version>/docker_init.sh

for example to initialise file_handle version 0.1.1, run:

src/nf_modules/file_handle/0.1.1/docker_init.sh

Running the tests

cd data
git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
cp data/tiny_dataset/fastq/tiny_R1.fastq data/tiny_dataset/fastq/tiny2_R1.fastq
cp data/tiny_dataset/fastq/tiny_R2.fastq data/tiny_dataset/fastq/tiny2_R2.fastq
cp data/tiny_dataset/fastq/tiny_S.fastq data/tiny_dataset/fastq/tiny2_S.fastq
nextflow src/nf_test.nf -c src/nf_test.config --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"

Explain how to run the automated tests for this system

Break down into end to end tests

Explain what these tests test and why

Give an example

And coding style tests

Explain what these tests test and why

Give an example

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Laurent Modolo - Initial work

See also the list of contributors who participated in this project.

License

This project is licensed under the CeCiLL License- see the LICENSE file for details