NAME

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

SYNOPSIS

     biox run -w workflow.yml
     biox -h

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 --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

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 <[email protected]>

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

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