BioX::Workflow::Command - Opinionated Bioinformatics Genomics Workflow Creator
biox run -w workflow.yml biox -h
Full documentation is available at gitbooks. [Documentation ](https://metacpan.org/pod/ https:#biosails.gitbooks.io-biox-workflow-command-docs-content)
#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
BioX::Workflow::Command is a templating system for creating Bioinformatics Workflows.
Jillian Rowe firstname.lastname@example.org
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.