Merge pull request common-workflow-language#706 from common-workflow-…

…language/skip-validation

Add flag to skip validation.

V1.1.0-dev1 support (common-workflow-language#694)

Support for v1.1.0-dev1 end of March milestone.

Fix exec_js_process process caching (common-workflow-language#701)

* Fix exec_js_process process caching

The existing logic doesn't properly cache processes, leading to a new process being created for every invocation of `exec_js_process` (eventually leading to an error due to too many processes with many calls to execjs). This commit fixes this logic and adds tests for this.

Add javascript code snippet validation (common-workflow-language#662)

* Add validation for javascript expressions.

Fixes common-workflow-language#594. To do this, it is needed to add jshint and refractor
js_sandbox to so that it can be useful for this.

Experimental extension for "secret" parameters. (common-workflow-lang…

…uage#683)

* Experimental extension for "secret" parameters.

These are string input parameters that represent sensitive information
such as passwords.  This feature deliberately obscures them by
replacing them with a placeholder during workflow evaluation and then
substituting the real value at the last moment.  Staged files containing secrets are deleted when the tool completes.

Merge pull request common-workflow-language#684 from common-workflow-…

…language/better_backward_compat

add default value for compute_checksum

Merge pull request common-workflow-language#652 from wtsi-hgi/fix-648

Fix common-workflow-language#628 and improve parameter reference error messages

Merge pull request common-workflow-language#617 from common-workflow-…

…language/singularity-support

Singularity support

Merge pull request common-workflow-language#641 from common-workflow-…

…language/fix/any-compatibility

Fix Any type compatibility in outputSource for workflows

Merge pull request common-workflow-language#634 from common-workflow-…

…language/v1.1/empty-array-input

Do not add anything to command line if input array is empty