File Reference
This documentation provides a comprehensive guide to the template structure necessary for implementing File Reference objects. These objects enable users to codify information to track and version the reference files used by the pipeline.
Template
## File Reference information ###############################
# Information for reference file
#############################################################
# All the following fields are required
name: <string>
description: <string>
format: <format> # bam, fastq, bwt, ...
version: <string>
# All the following fields are optional and provided as example,
# can be expanded to anything accepted by the schema
# https://github.com/dbmi-bgm/cgap-portal/tree/master/src/encoded/schemas
secondary_files:
- <format> # bam, fastq, bwt, ...
status: <status> # uploading, uploaded
license: <string> # MIT, GPLv3, ...
# Required to enable sync with a reference bucket
uuid: <uuid4>
accession: <accession>
Fields Definition
Required
All the following fields are required.
name
Name of the reference file, MUST BE GLOBALLY UNIQUE (ACROSS THE PORTAL OBJECTS).
description
Description of the reference file.
format
File format used by the reference file.
<format> needs to match a file format that has been previously defined, see File Format.
version
Version of the reference file.
Optional
All the following fields are optional and provided as example. Can be expanded to anything accepted by the schema, see schemas.
secondary_files
List of <format> for secondary files associated to the reference file.
Each <format> needs to match a file format that has been previously defined, see File Format.
status
Status of the upload.
The possible values are uploading and uploaded.
If no value is specified, the status will not be updated during patching and set to uploading if posting the object for the first time.
Most likely you don’t want to set this field and just use the default logic automatically applied during deployment.
license
License information.