[ensembl-dev] VEP plugin execution order

[Graham Ritchie]

Hi Michael,

Yes, plugins are run in the order in which they are specified on the command line or ini file, so they can be run as a pipeline, with, for example, a later plugin filtering output based on the results from an earlier plugin. However, if you are using the filtering mechanism (by returning undef rather than a hashref from the run method), the first plugin to filter a line 'wins' and no further plugins will be run on that line.

Cheers,

Graham


On 21 Jan 2012, at 23:10, Michael Yourshaw wrote:

> It looks like VEP plugins get called in the same order as listed in the command line parameters or ini file. Can I rely on this behavior?
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> Michael Yourshaw
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