RNAflow
Authors
- Rachel Legendre (@rlegendr)
What is RNAflow ?
RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis @Hub of Bioinformatics & Biostatistics.
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
- alienTrimmer
- fastqc
- sortmeRNA
- samtools
- bowtie2
- bedtools
- star
- minimap2
- kallisto
- 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: Load your conda environment
See runme.sh to create the complete conda env.
conda activate snakemake
- Step 4: Execute workflow
Test your configuration by performing a dry-run via
snakemake -n
run it in a Maestro using environment modules via
sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --use-envmodules --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --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