Create biocompute logs — write

BioCompute is a standard for logs of programs for for Bioinformatics Computational Analyses.

The BioCompute object is a json log that can be created based on the output of run().

Usage

write_biocompute(queue = run("_whirl.yml"), path = "bco.json", ...)

queue: Result from run().
path: A character string specifying the file path to write BioCompute log to.
...: Additional arguments parsed to jsonlite::write_json(). Note always uses auto_unbox = TRUE.

(invisible) list of the biocompute domains and their content.

The object consists of the following domains:

Specifications:
- spec_version: Version of BioCompute used (`https://w3id.org/biocompute/1.3.0/“)
- object_id: Unique project id
- type: Your project type
- etag: Your etag id from the BioCompute Object Portal
Provenance Domain
- This is used to track the history of the BCO. Review and signatures go here.
Usability Domain
- This is used to improve searchability by allowing a free-text description of the BCO.
- Provide external document.
Extension Domain
- This is used to add any additional structured information that is not directly covered by the BCO.
Description Domain
- Contains a structured field for the description of external references, the pipeline steps, and the relationship of I/O objects.
- Provide external document.
Execution Domain
- Contains fields for the execution of the BCO.
Parametric Domain
- Represents the list of parameters customizing the computational flow which can affect the output of the calculations.
IO Domain
- Represents the list of global input and output files created by the computational workflow.
Error Domain
- Defines the empirical and algorithmic limits and error sources of the BCO.