https://github.com/biosails/biox-workflow-command

https://github.com/biosails/biox-workflow-command

Last synced: 8 months ago
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• Host: GitHub
• URL: https://github.com/biosails/biox-workflow-command
• Owner: biosails
• License: other
• Created: 2017-01-05T08:40:34.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2018-07-02T17:06:14.000Z (almost 8 years ago)
• Last Synced: 2023-10-29T11:28:49.509Z (over 2 years ago)
• Language: Perl
• Size: 297 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • Changelog: Changes
  • License: LICENSE

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README

          
# 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 ](https://metacpan.org/pod/

https:#biosails.gitbooks.io-biox-workflow-command-docs-content)

# 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 

# 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