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BCO Execution

Repository to share data, workflows, apps, and scripts working toward the goal of execution of BioCompute Objects (BCO).

Lifecycle: maturing License: AGPL-3.0

summary

This repository also includes two example workflows that can be used to generate a BCO. One, is a simple CWL tool definition using the common NGS quality control program fastqc. The second is a part of the GATK workflows, the Broad Best Practice Data Pre-processing Workflow. This workflow is intended to prepare whole-exome or whole-genome sequencing data for variant calling. The included workflow is publicly available from the Broad and Seven Bridges' public Open Workflows repository here. It has been packed into a single .cwl file for convenience. The included .yml files describe jobs that were validated through cwltool and toil.

Usage Notes

This repository include all the required apps/tools to crate BCO from scratch or CWL workflow, and provides an easy-to-use script to validate and excute given BCO with provided workflow language in its 'Execution Domain'.

Begin by cloning the repo to your local machine.

Software requirements

BCO APP Installation

Getting the BCO R Shiny app

  1. Navigate to the BCO App Github Page: https://github.com/sbg/bco-app
  2. Clone the repo, or follow the directions for running through the Docker container

Using the Docker version is recommended unless doing development work on the BCO App itself.

BCO Runner Script Installation [1]

To install:

Clone the repository and install the enviroment:

git clone https://github.com/skoc/BCO-Execution.git

cd BCO-Execution/bco_runner

Create a conda environment from it as follows:

conda env create -f environment.yml

conda activate bco

Supported commands:

python bco_runner.py --help

positional arguments:
  {functions,license,validate,run_cwl}
    functions           list all available functions
    license             Prints BCO License
    validate            Validation options. Used to test a BCO against a JSON
                        schema. If no schema is supplied the ieee-2791-schema
                        is used as the default
    run_cwl             run a CWL

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Validate BCO

python bco_runner.py validate -b <BCO_FILE>

Run CWL of BCO

python bco_runner.py run_cwl -b <BCO_FILE>

References

  1. bcotool by Hadley King

  2. BioCompute Objects