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RNAflow

Snakemake Python 3.6

Authors

What is RNAflow ?

RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis. Be careful, RNAflow was principally conceived to run on the HPC of Institut Pasteur, and not on other HPC.

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
  • multiqc

For Institut Pasteur HPC users, these tools are not required, they will be automatically loaded via module during pipeline running via the snakemake --use-envmodules instruction.

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