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rnaflow

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    config
    workflow
    LICENCE
    README.md
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    RNAflow

    Snakemake Python 3.6

    Authors

    What is RNAflow ?

    RNAsig is a snakemake pipeline dedicated to standard transcriptomic analysis.

    How to install RNAflow ?

    You need to install:

    • snakemake >= 5.10
    • python >= 3.6

    In addition to above tools, you need to install pipeline-related tools:

    • cutadapt
    • fastqc
    • samtools
    • bowtie2
    • bedtools
    • star
    • deeptools

    How to run RNAflow ?

    Usage

    • Step 1: Install workflow

    If you simply want to use this workflow, download and extract the latest release.

    git clone https://gitlab.pasteur.fr/hub/rnaflow.git

    • Step 2: Configure workflow

    Configure the workflow according to your needs via editing the config.yaml and multiqc_config.yaml files in the config/ directory.

    • Step 3: Execute workflow

    Test your configuration by performing a dry-run via

    snakemake -n

    run it in a HPC using environment modules via

    snakemake -s Snakefile --use-envmodules --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock

    Visualize how the rules are connected via

    snakemake -s Snakefile --rulegraph --nolock | dot -Tsvg > rulegraph.svg

    or how the files are processed via

    snakemake -s Snakefile -j 10 --dag --nolock | dot -Tsvg > dag.svg