What was the Catholic Church's role in the Spanish Inquisition?

Although the Spanish Inquisition was partly an attempt to
force people to adhere to the beliefs and practices of the Catholic Church, it was not
really under the control of the Church.  Instead, it was run autonomously by Ferdinand
and Isabella, the King and Queen of Spain.

The main purpose
of the Spanish Inquisition was to root out people who were pretending to be Christian
but were secretly Jewish or Muslim.  The Spanish monarchs felt that this needed to be
done for a number of reasons.  As the link below
says:

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Apparently, the monarchs acted from several
motivations: They wanted to save souls from condemnation, to promote religious
conformity, to centralize their political control, to appease public prejudices, and
also to raise funds.

The Pope
gave permission for the Inquisition to begin and proceed, but was not in control of it. 
Instead, it was the King and Queen, heavily influenced by the Dominican order, who were
in control.

Therefore, the role of the Catholic Church was
limited.  The Inquisition was carried out by priests.  However, they were not acting
under the direction of the Church hierarchy but rather under the direction of the
Spanish crown.