Kevin Sayers
Kevin Sayers
When the JS inputs get parsed currently they do not work correctly. In CWL the scatter results in a single input for a given name. The parser currently parses everything...
Add parsing for environment variables from CWL this will then map to Nextflow variables of the style env.foo ``` cwlVersion: v1.0 class: CommandLineTool baseCommand: env requirements: EnvVarRequirement: envDef: HELLO: $(inputs.message)...
Update the input parsing such that inputs are added as keys into the JS dictionary. This enables the evaluation of code such as the below. ``` $(inputs.foo) ```
secondaryFile can also be used as an output (?).
Determine how CWL would handle a default value of null for an input. The input might be dropped entirely. Currently the parser makes null objects into a null string, but...
Add support for CWL secondary files. These files are files which must be present in the processing folder, but are not necessarily inputs. In nextflow these files should just be...
The input parameters must currently be provided in YAML, though CWL supports both YAML and JSON. Implementing a JSON parser should be easier for the parameters file as the number...
Currently the converter does not handle the CWL style shown below, only CWL that lacks - id will parse correctly. Also the input file can only be in YAML, JSON...
Add in support for directory arrays as input/outputs.