[Bioperl-pipeline] Plant-Biotech pipeline

[Joachim H. Strach]

Hello,

first of all thanks for your previous anwsers, they helped a lot for my understanding of the Biopipe workflow.

Some more question arised ... .
I would be glad if either you could tell me to find the suitable documentation or  give me some more answers.

I took a closer look to genome_annotation_pipeline.xml:
- What are the tags <transformer>, <input_iohandler_mapping>, good for?
- What is the function of the <data_monger> ?
- At the rule section in <action>: where is e.g. the "COPY_ID" related to?

- Shawn, why did you say "... return mostly bioperl objects". Which runnables do not and what do they return?
- My pipeline should perform two blast queries, where the second one gets as input the filtered ouput of the first one.  How can I filter on the bioperl objects directly without using IO-handling?  Or more general:  How can I pass on the bioperl objects returned from a runnable to the runnable of the next analysis?

Thanks for your advice.

Joachim







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