NanoSnake is a collection of Snakemake pipelines neatly wrapped in a convenient python package interface. It is easy to install with conda and to simple to run on a local computer or in a cluster environment.

Conda is the only dependency that you need to install the package.

All the other packages and external program needed for this pipeline will then be automatically handled by conda itself.

Install conda following the official documentation for you system

https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

You might not need all the extra channels depending on you conda configuration, but you need to add at least my channel: aleg

conda create -n nanosnake -c aleg -c anaconda -c bioconda -c conda-forge python=3.6 nanosnake

conda activate nanosnake

To update the package, from the package directory

conda activate nanosnake

conda update nanosnake -c aleg

At the moment there is only 2 workflows available in NanoSnake:

• DNA_ONT : Analyse Basecalled Nanopore sequencing data.

  • Download and cleanup genome
  • Fastq merging and filtering
  • Alignment with minimap2
  • Alignment cleaning
  • Generate coverage plots IGV and bedgraph (optional)
  • Run Nanopore QC with pycoQC (optional)
  • Run DNA methylation analysing with Nanoplolish + pycoMeth (optional)
  • Run SV analysis with Sniffles + pycoSV (optional)

• RNA_illumina : Analyse Illumina long RNA-seq sequencing data.

  • Download and cleanup genome, transcriptome and annotations
  • Fastq filtering / control / pre-alignment quality control
  • Genome alignment with STAR
  • Summarize STAR counts for all samples
  • Alignment cleaning
  • Transcriptome pseudo-alignment and transcripts quantification with Salmon
  • Summarize Salmon counts for all samples
  • Generate coverage plots IGV and bedgraph (optional)
  • Count reads per genes with featurecounts and summarize counts for all samples (optional)
  • Calculation of FPKM with cufflinks and summarize FPKM for all samples (optional)

Generate the sample sheet and config template files required for the workflow you want to run.

conda activate NanoSnake

NanoSnake {WORKFLOW NAME} --generate_template config sample_sheet --overwrite_template

# Or for a cluster environment

NanoSnake {WORKFLOW NAME} --generate_template cluster_config sample_sheet --overwrite_template

The samples.tsv file needs to be filled with the required informations detailed in the file header and passed to NanoSnake (--sample_sheet).

The config.yaml can be modified and passed to NanoSnake (--config). It is generally recommended to stick to the default parameters.

The cluster_config.yaml can be modified and passed to NanoSnake (--cluster_config). Use the file instead of config.yaml if you are executing the pipeline in a cluster environment. By default the file is for an LSF cluster, but it can be modified for other HPC platforms.

Call NanoSnake and choose your workflow

conda activate NanoSnake

NanoSnake {WORKFLOW NAME} {OPTIONS}

Usage on a local machine

conda activate NanoSnake

NanoSnake DNA_ONT -r ref.fa  -s sample_sheet.tsv --config config.yaml --cores 10

Usage in an LSF cluster environment

Use the cluster_config option instead of the config file. The cluster_config provided with NanoSnake is configured to work on an LSF cluster environment It contains the "prototype bsub command" to be used by Snakemake bsub -q {cluster.queue} -n {cluster.threads} -M {cluster.mem} -J {cluster.name} -oo {cluster.output} -eo {cluster.error} as well as the maximal number of cores and nodes to use.

conda activate NanoSnake

NanoSnake DNA_ONT -r ref.fa -s sample_sheet.tsv --cluster_config cluster_config.yaml

This repository contains snakemake wrappers for NanoSnake.

Wrappers can also be used outside of NanoSnake in any Snakemake file by using the following option:

--wrapper-prefix https://raw.githubusercontent.com/a-slide/NanoSnake/master/NanoSnake/wrappers/

The package contains test data and integrated tests all the wrappers.

usage: NanoSnake tests [-h]
                       [--wrappers ...]]
                       [--keep_output] [--clean_output] [--cores CORES]
                       [--workdir WORKDIR] [--verbose | --quiet]

Test all the wrappers

optional arguments:
  -h, --help                    show this help message and exit
  --wrappers ...]               List of wrappers to test (default: all)
  --keep_output, -k             Keep temporary output files generated during tests (default: False)
  --clean_output, -c            clean all temporary output files generated during tests (default: False)
  --cores CORES, -j CORES       the number of provided cores (default: 1)
  --workdir WORKDIR, -d WORKDIR Path to the working dir where to deploy the workflow (default: ./)
  --verbose, -v                 Show additional debug output (default: False)
  --quiet, -q                   Reduce overall output (default: False)

The repository is archived at Zenodo. If you use NanoSnake please cite as follow:

Adrien Leger. (2019, July 30). a-slide/NanoSnake. Zenodo. http://doi.org/10.5281/zenodo.3352283

• Adrien Leger (@a-slide) - aleg {at} ebi.ac.uk