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/smaht-dac/smaht-portal/tree/main/src/encoded/schemas
secondary_formats:
  - <format>              # bam, fastq, bwt, ...

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.