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param_exists() returns 1 if the parameter is present and can be
substituted, 0 if it is absent, and undef if the substitution failed.
param_is_defined() returns 1 if the paramter is present and can be
substituted to a defined value, undef if the substitution fails, 0
otherwise.
param() returns the value if param_exists() returned true, undef otherwise.
param_required() is like param() but dies instead of returning undef.

If a parameter references another parameter via the substitution mechanism
and the latter is missing, Params will now die.

* version/2.3:
  Capture errors from reading files / running commands in JobFactory

* version/2.2:
  Capture errors from reading files / running commands in JobFactory

* version/2.1:
  Capture errors from reading files / running commands in JobFactory

* version/2.0:
  Capture errors from reading files / running commands in JobFactory

* version/1.9:
  Capture errors from reading files / running commands in JobFactory

bugfix: make sure Stretched mode still works with extended meaning of _funnel_dfr (which can be a string in top-level cases)

moved conditions into Switch node for compactness AND allowed generic configuration of record-based nodes

procedures.sqlite has been modified to work with SQLite 3.6.20 that had a bug -- thanks to Jan Vogel.

The modified SQL works fine in SQLite 3.7.14 and SQLite 3.8.5

We're using SQLite version 3.6.20 - somehow SQLite throws on this left join: 

LEFT JOIN analysis_base a USING(analysis_id)

However, this explicit LEFT join works for us and our SQLite installation: 

LEFT JOIN analysis_base a ON a.analysis_id = r.analysis_id

* refs/pull/ensembl-github/12:
  Die if the absence of Getopt:ArgvFile prevents parsing the arguments
  Report the command-line options that haven't been used.
  Made "Getopt::ArgvFile" optional
  Update init_pipeline.pl

They can '@file_of_options' arguments that were not loaded because
Getopt::Argv is not installed. They can also be "-key value" type of
arguments that were not found in the config file.

Need to explicitly call argvFile() when "required" instead of "used"