Skip to contents

Create biocompute logs

Source: R/biocompute.R
write_biocompute.Rd

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", ...)

Arguments

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.

Value

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

Details

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.

    • Note: Use of keywords and External_Reference entries are not yet implemented. To use fill out the entries manually after creating the BioCompute object.`

  • Execution Domain

    • Contains fields for the execution of the BCO.

    • Note: Use of external_data_endpoints not implemented. Fill out manually afterwards if needed.

  • 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.

    • Note: Use of this domain is not clearly defined. It is therefore always left empty in the current implementation. If you want to add content do so manually after creating the BCO.

See the BioCompute Object Portal and the BioCompute Objects Wiki for more information.