[Bioperl-pipeline] DataMonger

[Elia Stupka]

> ok my understanding was that, we decided to run datamonger as an
> analysis because of our implemenation (running it on nodes, taking
> case of failures..) but it is actually conceptualised as being a
> data-preprocessor to some particular runnable and so it should belong
> to that particular analysis.. do you see it in a different way..

Got you, agree. It is a data pre and post processor. Though I can see
easily how now that they've been made runnables we will end up using it
when and where we feel like it. So really it is a runnable just like
others are. After all filtering is a simple analaysis...

On a similar note, I was thinking in the long run we will need another
"fake" generic runnable which is a ScriptRunner. It needs its own table
because it will take a script with its own series of parameters (or can
overload the parameter field to contain scriptname.pl -bla -bla). Then we
can easily pipe the output file of one script into the next script and
thus ensure that if there are simple scripts that we don't want to convert
to runnables because they are basically flatfile-related things,we can
still put them neatly in the pipeline.

Elia

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