- Quick Start
- SEE ALSO
BioX::Workflow::Command - Opinionated Bioinformatics Genomics Workflow Creator
biox run -w workflow.yml
Full documentation is available at gitbooks. Documentation
#Global Help biox --help biox-workflow.pl --help #Help Per Command biox run --help
#Previously biox-workflow.pl --workflow workflow.yaml biox run -w workflow.yml #or --workflow biox-workflow.pl run --workflow workflow.yml
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
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 new rules to an existing workflow.
biox add -w workflow.yml --rules rule4
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
BioX::Workflow::Command is a templating system for creating Bioinformatics Workflows.
Jillian Rowe <email@example.com>
Copyright 2017- Jillian Rowe
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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.