pipelines

JSON array

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.

Basic pipeline information is stored in the main squirrel.json file, and complete pipeline information is stored in the pipeline subdirectory in the pipeline.json file.

JSON Variables

*required

Variable	Type	Description
ClusterType	string	Compute cluster engine (sge or slurm).
ClusterUser	string	Submit username.
ClusterQueue	string	Queue to submit jobs.
ClusterSubmitHost	string	Hostname to submit jobs.
CompleteFiles	JSON array	JSON array of complete files, with relative paths to analysisroot.
CreateDate	datetime	Date the pipeline was created.
DataCopyMethod	string	How the data is copied to the analysis directory: cp, softlink, hardlink.
DependencyDirectory	string
DependencyLevel	string
DependencyLinkType	string
Description	string	Longer pipeline description.
DirectoryStructure	string
Directory	string	Directory where the analyses for this pipeline will be stored. Leave blank to use the default location.
Group	string	ID or name of a group on which this pipeline will run
GroupType	string	Either subject or study
Level	number	subject-level analysis (1) or group-level analysis (2). REQUIRED
MaxWallTime	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.
PipelineName	string	Pipeline name. REQUIRED
Notes	string	Extended notes about the pipeline
NumberConcurrentAnalyses	number	Number of analyses allowed to run at the same time. This number if managed by NiDB and is different than grid engine queue size.
ClusterNumberCores	number	Number of CPU cores requested for a running job.
ParentPipelines	string	Comma separated list of parent pipelines.
ResultScript	string	Executable script to be run at completion of the analysis to find and insert results back into NiDB.
SubmitDelay	number	Delay in hours, after the study datetime, to submit to the cluster. Allows time to upload behavioral data.
TempDirectory	string	The path to a temporary directory if it is used, on a compute node.
UseProfile	bool	true if using the profile option, false otherwise.
UseTempDirectory	bool	true if using a temporary directory, false otherwise.
Version	number	Version of the pipeline.
PrimaryScript	string	See details of pipeline scripts
SecondaryScript	string	See details of pipeline scripts.
VirtualPath	string	Path of this pipeline within the squirrel package.
DataStepCount	number	Number of data steps.
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/<PipelineName>