# pipelines Pipelines are the methods used to analyze data after it has been collected. In other words, the experiment provides the methods to collect the data and the pipelines provide the methods to analyze the data once it has been collected.

### JSON Variables :blue\_circle: Primary key\ :red\_circle: Required\ :yellow\_circle: Computed (squirrel writer/reader should handle these variables)

Variable	Type	Default	Description
`ClusterEngine`	string		Compute cluster engine (sge or slurm).
`ClusterQueue`	string		Queue to submit jobs.
`ClusterUser`	string		Submit username.
`ClusterMaxWallTime`	number		Maximum allowed clock (wall) time in minutes for the analysis to run.
`ClusterMemory`	number		Amount of memory in GB requested for a running job.
`ClusterNumberCores`	number	`1`	Number of CPU cores requested for a running job.
`ClusterNumberConcurrentAnalyses`	number	`1`	Number of analyses allowed to run at the same time. This number if managed by NiDB and is different than grid engine queue size.
`ClusterSubmitDelay`	number		Delay in hours, after the study datetime, to submit to the cluster. Allows time to upload behavioral data.
`ClusterSubmitHost`	string		Hostname to submit jobs.
`PipelineAnalysisLevel`	number	🔴	subject-level analysis (1) or group-level analysis (2).
`PipelineCompleteFiles`	JSON array		JSON array of complete files, with relative paths to `analysisroot`.
`PipelineCreateDate`	datetime	🔴	Date the pipeline was created.
`PipelineDescription`	string		Longer pipeline description.
`PipelineDirectory`	string		Directory where the analyses for this pipeline will be stored. Leave blank to use the default location.
`PipelineDirectoryStructure`	string
`PipelineName`	string	🔴 🔵	Pipeline name.
`PipelineNotes`	string		Extended notes about the pipeline
`PipelinePrimaryScript`	string	🔴	See details of pipeline scripts
`PipelineSecondaryScript`	string		See details of pipeline scripts.
`PipelineResultScript`	string		Executable script to be run at completion of the analysis to find and insert results back into NiDB.
`SetupDataCopyMethod`	string		How the data is copied to the analysis directory: `cp`, `softlink`, `hardlink`.
`SetupDependencyDirectory`	string		Where the dependency pipeline is placed relative to the analysisroot. `root` or `subdir`
`SearchDependencyLevel`	string
`SearchDependencyLinkType`	string
`SearchGroup`	string		ID or name of a group on which this pipeline will run
`SearchGroupType`	string		Either subject or study
`SearchParentPipelines`	string		Comma separated list of parent pipelines.
`SetupTempDirectory`	string		The path to a temporary directory if it is used, on a compute node.
`SetupUseProfile`	bool		true if using the profile option, false otherwise.
`SetupUseTempDirectory`	bool		true if using a temporary directory, false otherwise.
`Version`	number	`1`	Version of the pipeline.
`DataStepCount`	number	🟡	Number of data steps.
`VirtualPath`	string	🟡	Path of this pipeline within the squirrel package.
data-steps	JSON array		See data specifications

### Directory structure Files associated with this section are stored in the following directory. `PipelineName` is the unique name of the pipeline. > `/pipelines/` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/pipelines.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.