FileSet

Summary of SMaHT Portal object type FileSet . Types referencing this type are: AlignedReads, OutputFile, SubmittedFile, SupplementaryFile, UnalignedReads, VariantCalls. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.

Description: A FileSet item consists of the files produced from sequencing a library. Note: each library generated requires its own unique associated FileSet.

Tip

See actual FileSet data here

Required Properties

Property	Type	Description
libraries	Library array of string	See below for more details.
sequencing	Sequencing string	See below for more details.
submission_centers	SubmissionCenter array of string	See below for more details. See values here
submitted_id	string	See below for more details.

Identifying Properties

Property	Type	Description
accession	string	See below for more details.
submitted_id	string	See below for more details.
uuid	string	See below for more details.

Reference Properties

Property	Type	Description
consortia	Consortium array of string	See below for more details. See values here
files	File array of string	See below for more details.
libraries	Library array of string	See below for more details.
meta_workflow_runs	MetaWorkflowRun array of string	See below for more details.
protocols	Protocol array of string	See below for more details.
samples	CellSample array of string	See below for more details.
sequencing	Sequencing string	See below for more details.
submission_centers	SubmissionCenter array of string	See below for more details. See values here

Properties

Property	Type	Description
accession	string	A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.]
alternate_accessions	array of string • restricted	Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.]
comments	array of string • restricted	Additional comments on file set.
consortia	Consortium • array of string • unique	Consortia associated with this item. See values here
description	string	Plain text description of the item.
display_title	string • calculated	-
file_group	object • calculated	Object tag for files that are candidates for merging.
file_group . assay	string	-
file_group . sample_source	string	-
file_group . sequencing	string	-
file_group . submission_center	string	-
files	File • array of string • calculated	-
libraries	Library • array of string • min items: 1 • unique	Link to associated libraries.
meta_workflow_runs	MetaWorkflowRun • array of string • calculated	-
protocols	Protocol • array of string • min items: 1 • unique • restricted	Protocols providing experimental details.
samples	CellSample • array of string • min items: 1 • unique	Link to associated samples. Only to be used for single-cell data sets when many samples are associated with a single library.
sequencing	Sequencing • string	Link to associated sequencing.
status  • deleted  • draft  • in review ← default  • obsolete  • public  • released  • restricted	enum of string • default: in review	-
submission_centers	SubmissionCenter • array of string • unique	Submission Centers that created this item. See values here
submitted_id	string	Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_FILE-SET_[A-Z0-9-_.]{4,}$
tags	array of string • min string length: 1 • max string length: 50 • unique • restricted	Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$
uuid	string	Unique ID by which this object is identified.