This documentation provides a comprehensive guide to the template structure necessary for implementing File Format objects. These objects enable users to codify file formats used by the pipeline.
## File Format information ##################################
# Information for file format
#############################################################
# All the following fields are required
name: <string>
extension: <extension> # fa, fa.fai, dict, ...
description: <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_formats:
- <format> # bam, fastq, bwt, ...
file_types:
- <filetype> # FileReference, FileProcessed, FileSubmitted
status: <status> # shared
All the following fields are required.
Name of the file format, MUST BE GLOBALLY UNIQUE (ACROSS THE PORTAL OBJECTS).
Extension used by the file format.
Description of the file format.
All the following fields are optional and provided as example. Can be expanded to anything accepted by the schema, see schemas.
List of secondary <format>
available for the file format.
Each <format>
needs to match a file format that has been previously defined.
File types that can use the file format.
List of <filetype>
. The possible values are FileReference
, FileProcessed
and FileSubmitted
.
Default value if not specified is FileReference
and FileProcessed
.