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 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