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File specifications

master.yaml

The master.yaml file is the main source of information that RefChef uses to retrieve references, indices, and annotations. It is composed of sequences of code blocks that correspond to each reference. Each code block in master.yaml starts with a key, followed by metadata and levels.

See the master.yaml overview and usage for more information.

The key section consists of:

<reference_name>:
Expected format: String where <reference_name> is the name of the reference.

The metadata section consists of:

metadata.name
Expected format: <reference_name> string, should be the same as the block's key

metadata.common_name
Expected format: string

metadata.ncbi_taxon_id
Expected format: integer, based on NCBI taxon ID

metadata.organism
Expected format: string

metadata.organization
Expected format: string

metadata.custom
Expected format: string

metadata.description
Expected format: string

metadata.downloader
Expected format: string

metadata.ensembl_release_number
Expected format: integer

metadata.accession.genbank
Expected format: string

metadata.accession.refseq
Expected format: string

The levels section consists of:

levels.<type>
Where <type>: references, annotations, or indices

levels.<type>.- component
Expected format: string

levels.<type>.complete.status
Expected format: boolean (note that if complete.status is set to true RefChef will skip the current block and not retrieve any file. RefChef automatically changes the status to true after retrieving files for the first time.)

levels.<type>.src
Expected format: UUID string from existing reference, when adding an index file for a reference RefChef will create a symlink to the index files in the reference folder.

levels.<type>.commands
Expected format: Each command should start with -, this section is a list of commands to download and process each reference.

After refchef-cook is run and references are downloaded, levels.<type>.complete.status: false will change to levels.<type>.complete.status: true and the following fields will be added to master.yaml

levels.<type>.complete.time
Expected format: RefChef will autopopulate this field with the date and time stamp the reference was downloaded if levels.<type>.complete.status: true

levels.<type>.location
Expected format: Refchef will autopopulate this field with the directory where downloaded files are stored if levels.<type>.complete.status: true

levels.<type>.files
Expected format: Refchef will autopopulate this field with a list of files that were downloaded if levels.<type>.complete.status: true

levels.<type>.uuid
Expected format: Refchef will autopopulate this field with a UUID for your reference file if levels.<type>.complete.status: true

cfg.yaml

If using a cfg.yaml file, the cfg.yaml file should follow the following specs:

config-yaml.path-settings.reference-directory Expected format: String, path to reference storage directory

config-yaml.path-settings.git-directory Expected format: String, path to local git repository

config-yaml.path-settings.remote-repository Expected format: String, remote git repository, should be in the format of user/repo

config-yaml.log-settings.log Expected format: String, should be either 'yes' or 'no' in single quotes, indicating whether or not log files will be made

Also see the cfg.yaml overview and example.

cfg.ini

If using a cfg.ini file, the cfg.ini file should follow the following specs:

[path-settings].reference-directory=
Expected format: String, path to reference storage directory

[path-settings].git-directory=
Expected format: String, path to local git repository

[path-settings].remote-repository=
Expected format: String, remote git repository, should be in the format of user/repo

[log-settings].log=
Expected format: String, should be either 'yes' or 'no', indicating whether or not log files will be made

[runtime-settings].break-on-error=
Expected format: String, should be either 'yes' or 'no', indicating how RefChef should respond when encountering an error

[runtime-settings].verbose=
Expected format: String, should be either 'yes' or 'no', toggles between verbosity output settings

Also see the cfg.ini overview and example.