Make "standard" miRNA and piRNA pipelines from the smallRNA-seq pipelines

[ssayols]

Generalize the miRNA-seq and piRNA-seq pipelines.

Also, some extra work needs to be done in these pipelines:

• Use the general tool tree, instead of custom installations
• Reuse bpipe modules when possible. Currently, many are hard-copies of modules in other categories
• Adapt to the new architecture