Using GGD in Workflows

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Important

If you use GGD, please cite the Nature Communications GGD paper

GGD and Workflows

Another advantage of GGD is its ability to be used in different workflows. These workflows can range from simple to complex, as well as from a bash script style workflow to more advance worflow managers like Snakemake and Nextflow.

It is customary that data is required and used during a workflow. Rather then having to store and transmit that data along with a workflow, one could create the workflow with GGD data packages as dependencies and allow GGD to dynamically provide the data to the workflow.

GGD can be used before running a workflow or during the workflow process. Additionaly, data recipes can be installed into a Docker or Singularity container, where a workflow like Netxflow uses the conda software packages and the GGD data packages in the container during the workflow process. GGD can be used during the workflow to install the required package into a specific environment if those packages are not yet installed. This allows versitlity in the use of GGD for many types of workflows.

Provided below are two examples of using GGD in a workflow. These are two simple exmaples and don’t fully show the extent of what can be done with GGD wihtin a workflow, but rather stand as starting examples of what can be done.

Snakemake Workflow Example

Nextflow Workflow Example

Contents:

• Snakemake Workflow with GGD
  • Workflow Files
  • Alternative Approaches
  • Workflow Output Examples:
• Nextflow Workflow with GGD
  • Nextflow Workflow Files
  • Steps to run the workflow
  • Results: