# Definitions **Annotations:** Data describing the gene models, pathways, ontologies, and other relevant biological information. Annotations are always associated with a reference genome and are consumed during a command execution through the argument or input variables. **Argument(s):** Parameter variables that are defined with a key-value pair (*Example: --Threads 10*). Arguments are used by the tools during command building. **Command:** Fundamental unit of a tool that executes a specific job. **Data Store:** Stores all data types uploaded into the user's account. The data store is subdivided (sequence data, references, annotations, and metadata) for easy access. **Execution Flow:** Displays the list of tools in the execution order **FileList:** List of files used by a tool/command **File:** A single file used by a tool/command **Metadata:** Data that describes an experiment. Metadata is used for data analysis through the options, argument, or input variables. **Merge Step:** A step in a pipeline that merges all the input files into a single output file. **My Pipelines:** Pipelines shown within a project. Pipelines can be copied from the Pipeline Library into a project. **Hub:** Pipelines are grouped into categories (Hub) based on function. **Input(s):** Any data files used in a command. These are either uploaded by the user or generated within an executed job. **Jobs:** Each execution of a pipeline is designated with a job ID. **Option(s):** Command parameters that are defined with a single word (*Example: --ignore*). These are used by the tools while command building. **Output(s):** Data files created during pipeline execution. **Pipeline:** A set of computational tools, which run either sequentially or parallelly in order to achieve a specific data analysis objective. Tools/commands are designated as steps in a pipeline. **Pipeline Library:** The list of pre-configured pipelines available on the platform **Projects:** Self-contained mini-workspaces, where sample sets can be analyzed independently without interference from other data, using multiple pipelines. **Reports:** Results of a pipeline execution are aggregated into easily understandable formats for quick viewing. **Sample Set:** A set of samples (cohort) selected within a project. Sample sets are used for data analysis. **Tool:** A bioinformatics software program that solves a specific biological problem. A tool can contain multiple commands (Example: Samtools index, sort)