Examples

This section provides a growing collection of examples that demonstrate how to use ZARP-cli in various scenarios.

Prerequisites

The examples below assume that you have already installed and initialized _ZARP-cli.

Process samples deposited to SRA

Let's have ZARP-cli fetch two samples from SRA, infer all necessary metadata, fetch the corresponding genome annotations and start a ZARP workflow run on them:

zarp SRR23590181 SRR23529108

I want to verify the inferred metadata first!

Set the --execution-mode parameter to PREPARE_RUN to run ZARP-cli up until the point of the actual ZARP workflow execution:

zarp --execution-mode=PREPARE_RUN SRR23590181 SRR23529108 

More please!

You will find a description of more elaborate use cases in the ZARP publication and the accompanying supplementary materials, published on Zenodo. The latter include detailed instructions, all necessary input files and a selection of reference output files to validate your runs against.