ccwl 0.3.0

Changes in 0.3.0 (since 0.2.0)

Features

• New array construct to specify array types
• Allow specification of array input item separators
• New pass-through identity construct
• New scattering scatter, scatter-cross and scatter-nested-cross constructs
• New #:stdout and #:stderr parameters in commands

Support staging input files

• Support returning command objects, not just workflow objects, from ccwl files
• Allow literal values as arguments
• Add message requesting users report uncaught exceptions as bugs
• Allow steps with expressions that evaluate to commands
• Allow steps with unspecified default arguments
• Support specifying command requirements
• Tolerate prefixed strings in #:run parameters of commands
• Allow calling workflows inside other workflows
• Deprecate auto-connection of single-input commands

Compiler error messages

ccwl now comes with significantly better error messages that highlight the exact context of errors in workflow descriptions.

• Error out if arguments have been supplied more than once
• Error out when ccwl file does not return supported object
• Error out when unknown keys were passed to rename
• Error out when workflow syntax is not recognized
• Error out when body of workflow has multiple expressions
• Error out on unrecognized keyword arguments to command, input or output
• Error out on unexpected extra argument to unary keyword argument of command, input or output
• Error out on unexpected positional argument to command, input or output
• Error out when external CWL workflow files do not exist
• Error out when undefined inputs are used in the #:run parameter of a command
• Error out when command is not defined
• Error out on argument prefixes that are not strings
• Error out when #:other and #:binding parameters are not YAML serializable trees
• Error out when workflow step is missing required parameters
• Error out when workflow step does not accept input key
• Error out when workflow step is supplied with unknown key
• Error out when #:run argument to command is invalid
• Error out when rename mappings are not an alternating sequence of keywords and symbols

Noteworthy bug fixes

• Escape all indicator characters when serializing YAML
• Do not escape backslashes when serializing graphviz dot
• When key is renamed, rename the corresponding CWL output ID too
• Rename final workflow output correctly

Other

• Serialize atomic YAML dictionary values on the same line
• Serialize YAML arrays with a single atomic value on the same line
• New guile-lib dependency for (term ansi-color)