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  • nextflow pipeline

    This repository is a template and a library repository to help you build nextflow pipeline. You can fork this repository to build your own pipeline. To get the last commits from this repository into your fork use the following commands:

    git remote add upstream gitlab_lbmc:pipelines/nextflow.git
    git pull upstream master

    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 initialize a given tools run the following command:

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

    For example to initialize file_handle version 0.1.1, run:

    src/docker_modules/file_handle/0.1.1/docker_init.sh

    To initialize 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 training 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.sh

    For example to run the tests on Bowtie2 run:

    src/nf_modules/Bowtie2/tests.sh

    Available tools

    tool nf module docker module psmn module
    BEDtools ok ok ok
    BFCtools no ok ok
    bioawk no ok ok
    Bowtie ok ok no
    Bowtie2 ok ok ok
    BWA ok ok ok
    canu ok ok ok
    cutadapt ok ok ok
    deepTools ok ok ok
    FastQC ok ok ok
    file_handle no ok ok
    GATK no ok ok
    HISAT2 no ok no
    HTSeq ok ok ok
    Kallisto ok ok ok
    MACS2 no ok ok
    MultiQC ok ok ok
    MUSIC ok ok ok
    picard no ok ok
    pigz no ok ok
    RSEM ok ok ok
    sambamba ok ok ok
    samblaster ok ok ok
    SAMtools ok ok ok
    SRAtoolkit ok ok ok
    Salmon no ok ok
    TopHat no ok ok
    Trimmomatic no ok ok
    UrQt ok ok ok

    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