SeqWare/seqware — pull request #162 by morgantaschuk (2013-11-29 22:06:18+00:00)
Title: Feature/pde 428 update workflow archetype

Updated the workflow archetype, docs and tests.

The workflow Java class and INI file are named for the workflow. I reduced the number of things that you have to enter to initiate the archetype. Now cat and echo are used in the class, and properties are pulled from the INI file. I added in a useful method, 'createOutputFile' to the workflow class. I added docs throughout. The output files are now added to the Java job that creates them. The pom now has the maven-junction-plugin, and it properly moves the links folder over into the final bundle. I removed the data dir from the workflows directory accordingly.

I updated the docs with all the new features, and updated the tests so they hopefully pass.