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
• subread
• 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 on Maestro (Institut Pasteur HPC)

Load your conda environment. See runme.sh to create the complete conda env.

conda activate snakemake

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

• Step 3bis: Execute workflow on NNCR (IFB HPC)

Load all needed tools via module

module load snakemake/6.5.0
module load cutadapt/3.1
module load fastqc/0.11.9
module load singularity sortmerna/4.2.0
module load samtools/1.9
module load bowtie2/2.4.1
module load bedtools/2.29.2
module load star/2.6 
module load minimap2/2.18
module load kallisto/0.46.2
module load deeptools/3.5.0
module load subread/2.0.1
module load multiqc/1.11

Note that alienTrimmer is not installed in NNCR HPC yet.

Test your configuration by performing a dry-run via

snakemake -n -c 1

run it in NNCR using environment modules via

sbatch -c 8 snakemake --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 100 --nolock --cores 8