File Format

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.

Template

## 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

Fields Definition

Required

All the following fields are required.

name

Name of the file format, MUST BE GLOBALLY UNIQUE (ACROSS THE PORTAL OBJECTS).

extension

Extension used by the file format.

description

Description of the file format.

Optional

All the following fields are optional and provided as example. Can be expanded to anything accepted by the schema, see schemas.

secondary_formats

List of secondary <format> available for the file format. Each <format> needs to match a file format that has been previously defined.

file_types

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.