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