If you want to write pipelines, you probably need efficient and specialized programs to perform processing tasks. This calls for C development. However this is often a big effort, probably too much if you are considering chains of very simple operations to be automated. One solution is to script eclipse from a high-level scripting language, such as Python, Perl, Tcl, or Lua.
eclipse is distributed with two sets of bindings: for Python and Lua. These packages are for the moment experimental and little documented. Expect more in the next releases!