Flexible execution of pipeline

[ipurusho]

Allow user (via command line) be able to pick desired tasks to execute on seq data. Allows for flexibility for choosing seq analysis workflow, for complete or partial pipelines.

[ipurusho]

example:
completeseq {base_path} -m tophat -q -d limma -o /output/dir

executes mapping (m), quality control (q) and diff analysis (d) using tools of choice

[lishen]

It would be great to control the pipeline using a configuration file as well. This not only increases your productivity but also allows reproducible analysis.

[ipurusho]

That's a great idea. I'll add that to the issue list. This might be a better option because it will allow us to input all the necessary and optional run parameters of tophat, cuffdiff, etc. more easily.