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BU-ISCIII/SARS_Cov2_consensus-nf: Installation

To start using the BU-ISCIII/SARS_Cov2_consensus-nf pipeline, follow the steps below:

Install NextFlow

Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:

# Make sure that Java v8+ is installed:
java -version

# Install Nextflow
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

See nextflow.io for further instructions on how to install and configure Nextflow.

Install the pipeline

You'll need to download the repository from our GitHub:

wget https://github.com/BU-ISCIII/SARS_Cov2-nf/archive/master.zip
unzip master.zip -d ~/my-pipelines/

Pipeline configuration

By default, the pipeline loads a basic server configuration conf/base.config This uses a number of sensible defaults for process requirements and is suitable for running on a simple (if powerful!) local server.

Be warned of two important points about this default configuration:

  1. The default profile uses the local executor
    • See the nextflow docs for information about running with other hardware backends. Most job scheduler systems are natively supported.
  2. Nextflow will expect all software to be installed and available on the PATH
    • You can create a conda environment with all the programs needed for this pipeline with our environment.yml file. See below.

Conda

You can use conda to manage the software requirements. To use it first ensure that you have conda installed (we recommend miniconda). To create the environment you just have to run:

conda env create -f environment.yml

And the environment will be created in your machine with all the programs. NOTE: To run the pipeline with SARS-Cov2 data you will have to do the following steps to set snpEff SARS-Cov2 database:

cd /path/to/your/miniconda3/envs/virus_illumina/share/snpeff-4.3.1t-3 ##Run all the following commands in this folder
vim SnpEff.config ## Add new genome entry.
  sars-cov-2.genome : SARScov2
mkdir -p data/genomes
mkdir -p data/sars-cov-2
cp /path/to/reference/fasta/GCF_009858895.2_ASM985889v3_genomic.fna data/genomes/sars-cov-2.fa
cp /path/to/reference/fasta/GCF_009858895.2_ASM985889v3_genomic.gff data/sars-cov-2/genes.gff
java -jar snpEff.jar build -gff3 -v sars-cov-2