Snakemake workflow: DiCa

This workflow performs mapping and variant calling following GATK Best Practices for Germline Variant Discovery. DiCA is part of the Snakemake-based pipelines collection solida-core developed and manteined at CRS4.

Authors

• Matteo Massidda (@massiddaMT)
• Rossano Atzeni (@ratzeni)

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=6.15 snakedeploy

and activate it:

conda activate snakemake

We get some public data to test the pipeline. You can directly clone in this folder from github, just type:

git clone https://github.com/solida-core/test-data-DNA.git

You can then 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/solida-core/dica 
                    my_desd_dir 
                    --tag XXXX

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

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

You can generate analysis report with the command:

snakemake --report report.zip --cores all