Merge pull request #571 from georgebyelas/master

command-line refactoring
remove molgenis-app-omicsconnect, please use molgenis-app-omx
Merge pull request #574 from dennishendriksen/master

Remove molgenis-app-omicsconnect
Merge pull request #576 from georgebyelas/master

added extra parameter to specify backend credentials; make it run from database with pilots; issue #573
Merge pull request #578 from georgebyelas/master

solved issue with auto-generating id; issue #567; introduced autoid flag; now, jobs are starting to run if --run is present
Merge pull request #581 from georgebyelas/master

fix generation of tasks, which use parameters from command line in the parameters file; issue 580; tests are added
Merge pull request #584 from georgebyelas/master

one more test for using command-line parameters in parameters without recursion
Merge pull request #585 from georgebyelas/master

fixed issue #566; tests added
Merge pull request #587 from georgebyelas/master

added README.txt and generated .html file for Molgenis Compute (run acsiidoc, before commit new version)
Merge pull request #592 from georgebyelas/master

new version of documentation; few fixes in workflows and code
Merge pull request #593 from georgebyelas/master

direct link is removed, because it does not work
Merge pull request #596 from georgebyelas/master

	fix issues with molgenis header 590,586; added tests; change help exit; code refactoring all around
Merge pull request #600 from georgebyelas/master

started compute refactoring
Merge pull request #601 from georgebyelas/master

working version for testing; values replacement will be added soon
Merge pull request #603 from georgebyelas/master

added tests for folding ( follow instruction issue #602 incorrect folding, now called collapse bug)
Merge pull request #604 from georgebyelas/master

tests for folding combinations
removed lifelines temporarily from build
Merge pull request #605 from mswertz/lifelines

removed lifelines temporarily from build
Merge pull request #606 from georgebyelas/master

weaving design time variables
Merge pull request #607 from georgebyelas/master

new tests added for double mapping and commented out, because they are failing; issues #598 and #595