NAME

    BioX::Workflow::Command - Opinionated Bioinformatics Genomics Workflow
    Creator

SYNOPSIS

      biox run -w workflow.yml

documentation

    Full documentation is available at gitbooks. Documentation 

Quick Start

 Get Help

      #Global Help
      biox --help
      biox-workflow.pl --help
      #Help Per Command
      biox run --help

 Run a Workflow

      #Previously biox-workflow.pl --workflow workflow.yaml
      biox run -w workflow.yml #or --workflow
      biox-workflow.pl run --workflow workflow.yml

 Run a Workflow with make like utilities

    Using the option --use_timestamps will select only rules that have
    INPUT/OUTPUT that does not exist or has been modified since the last
    log.

      biox run --workflow workflow.yml --use_timestamps

    Using the option --auto_deps will create #HPC deps based on your
    INPUT/OUTPUTs - use this with caution. It will only work correctly if
    INPUT/OUTPUT is complete and accurate.

      biox run --workflow workflow.yml --auto_deps

    Option --make enables both --use_timestamps and --auto_deps

      biox run --workflow workflow.yml --make

 Create a new workflow

    This creates a new workflow with rules rule1, rule2, rule3, with a few
    variables to help get you started.

      biox new -w workflow.yml --rules rule1,rule2,rule3

 Add a new rule to a workflow

    Add new rules to an existing workflow.

      biox add -w workflow.yml --rules rule4

 Check the status of files in your workflow

    You must have defined INPUT/OUTPUTs to make use of this rule. If you
    do, biox will output a table with information about your files.

      biox stats -w workflow.yml

DESCRIPTION

    BioX::Workflow::Command is a templating system for creating
    Bioinformatics Workflows.

AUTHOR

    Jillian Rowe <jillian.e.rowe@gmail.com>

COPYRIGHT

    Copyright 2017- Jillian Rowe

LICENSE

    This library is free software; you can redistribute it and/or modify it
    under the same terms as Perl itself.

Acknowledgements

    As of version 0.03:

    This modules continuing development is supported by NYU Abu Dhabi in
    the Center for Genomics and Systems Biology. With approval from NYUAD,
    this information was generalized and put on github, for which the
    authors would like to express their gratitude.

    Before version 0.03

    This module was originally developed at and for Weill Cornell Medical
    College in Qatar within ITS Advanced Computing Team. With approval from
    WCMC-Q, this information was generalized and put on github, for which
    the authors would like to express their gratitude.

SEE ALSO

