GitLab

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"

* version/2.3:
  Updated cpanfile with the latest list of modules
  Travis should now be able to post things to our Slack channel
  /usr/bin/psql and scripts/all_tests.pl should be excluded from the coverage statistics
  Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)
  Removed leftovers from a previous conflict

* version/2.2:
  Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)

* version/2.1:
  Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)

* version/2.0:
  Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)

Check that the analysis is not BLOCKED before running a special-batch (i.e. runWorker with a job_id)

This is can be overriden with "-force 1"

Using Getopt::ArgvFile allows to pass long, complex commandline options via a file to init_pipeline.pl 
The format of the file is a key/value file :
--option value 
--option2 value2