pipelines
JSON array
Last updated
JSON array
Last updated
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.
Files associated with this section are stored in the following directory. PipelineName is the unique name of the pipeline.
/pipelines/<PipelineName>
Primary key Required Computed (squirrel writer/reader should handle these variables)
| Variable | Type | Default | 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).
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.
Notes
string
Extended notes about the pipeline
NumberConcurrentAnalyses
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.
ClusterNumberCores
number
1
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
1
Version of the pipeline.
PrimaryScript
string
See details of pipeline scripts
SecondaryScript
string
See details of pipeline scripts.
DataStepCount
number
Number of data steps.
VirtualPath
string
Path of this pipeline within the squirrel package.
JSON array