Snakemake workflow: RNA VariantCalling Docker

This workflow performs variant calling and annotation for bulk RNA-Seq samples.

Authors

• Matteo Massidda, University of Sassari

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

INSTRUCTIONS

Create a virtual environment with the command:

mamba create -c bioconda -c conda-forge --name snakemake snakemake=7.18.1 snakedeploy

and activate it:

conda activate snakemake

You can perform the pipeline deploy defining a directory my_dest_dir for analysis output and a pipeline tag for a specific version:

snakedeploy deploy-workflow https://github.com/massiddamt/rna_vc_docker.git 
                    my_desd_dir 
                    --tag v1.0.2

To run the pipeline, go inside the deployed pipeline folder and use the command:

snakemake --use-conda -p --cores all