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bedtools

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  • 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/docker_modules/<tool_name>/<tool_version>/docker_init.sh

    for example to initialise file_handle version 0.1.1, run:

    src/docker_modules/file_handle/0.1.1/docker_init.sh

    To initialise all the tools:

    find src/docker_modules/ -name "docker_init.sh" | awk '{system($0)}'

    Running the tests

    To run tests we first need to get a trainning set

    cd data
    git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
    cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq
    cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq
    cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq
    cd ..

    Then to run the tests for a given tools run the following command:

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

    for example to run the tests on Bowtie2 run:

    src/nf_modules/Bowtie2/tests/tests.sh

    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