BioX::Workflow - A very opinionated template based workflow writer.

Most of the functionality can be accessed through the biox-workflow.pl script.

biox-workflow.pl --workflow /path/to/workflow.yml

This module was written with Bioinformatics workflows in mind, but should be extensible to any sort of workflow or pipeline.

Please check out the full Usage Docs at BioX::Workflow::Usage

Alternately, check out the github pages at http://jerowe.github.io/BioX-Workflow-Docs/showcase.html. This format may be easier to read.

You shouldn't really need to look here unless you have some reason to do some serious hacking.

Moose attributes. Technically any of these can be changed, but may break everything.

This should really be in BioX::Wrapper

Path to workflow workflow. This must be a YAML file.

This is the default. The outer loop are the rules, not the samples

Default Value. The outer loop is samples, not rules. Must be set in your global values or on the command line --sample_based 1

If you ever have resample: 1 in your config you should NOT set this value to true!

This isn't ever used in the code. Its just there incase you want to persist objects across rules

It uses Moose::Meta::Attribute::Native::Trait::Hash and supports all the methods.

    set_stash     => 'set',
    get_stash     => 'get',
    has_no_stash => 'is_empty',
    num_stashs    => 'count',
    delete_stash  => 'delete',
    stash_pairs   => 'kv',

Load plugins as an opt

attributes read in from runtime

Attributes defined in the global section of the yaml file

Attributes defined in the rules->rulename->local section of the yaml file

Our bash string

bowtie2 -p 12 -I {$sample}.fastq -O {$sample}.bam

Name of the rule

Name of the previous rule

Subroutines can also be overriden and/or extended in the usual Moose fashion.

Starting point.

Load the workflow, additional classes, and plugins

Initialize the global_attr, make the global outdir, and find samples

use Config::Any to load configuration files - yaml, json, etc

Load plugins defined in yaml or on command line with --plugins with MooseX::Object::Pluggable

Load classes defined in yaml with Class::Load

Make the template for interpolating strings

Add our global key from config file to the global_attr, and then to attr

Deprecated: set_global_yaml

Add attributes to $self-> namespace

Evaluate the keys for variables using Text::Template {$sample} -> SampleA {$self->indir} -> data/raw (or the indir of the rule)

If variables are themselves hashes/array refs, leave them alone

After each rule is processe clear the $self->attr

There should be one key and one key only!

Clear the process attr

Deprecated: clear_process_vars

Initialize the process vars

Add the local attr onto the global attr

BioX::Workflow - A very opinionated template based workflow writer.

Jillian Rowe [email protected]

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.

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 bitbucket, for which the authors would like to express their gratitude.

Copyright 2015- Weill Cornell Medical College in Qatar

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.