There are few changes in defining an input or output in CWL command line tool.
- No need to use "-id" no more. Instead of an input/output can be defined as follow,
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- Type can be defined without the tag "type" as follow,
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- An array can be defined as "<CWLTYPE>[]", for example an Integer array can be defined as follow,
- Now the type "["null",int]" which means the parameter type can be either a null or an int, can be defined as follow,
cwl-utilities module is upgraded for these specifications. Main difference is the output of the YAML parser is changed. Previously inputs or outputs were mapped to an ArrayList but now it's a LinkedHashMap.
To be more specific, all of the following forms are correct:
ReplyDeleteThe following is formatted as one-liners because Blogger doesn't support formatting for comments.
inputs: [ id: input_1, type: array, items: string]
inputs: [ input_1: string[] ]
inputs: [ input_1: [ type: string[] ] ]
inputs: [ [ id: input_1, type: string[] ] ]
See also http://www.commonwl.org/v1.0/CommandLineTool.html#Introduction_to_v1.0
A nicer formatted version of this is at https://gitter.im/common-workflow-language/common-workflow-language?at=57a2cfd6836d2d02116281ea
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