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BioX-Workflow-Command-2.0.3
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/ BioX::Workflow::Command

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