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Tips and Tricks

Comments at top of file show in hover

When you hover over the path of a linked file in the run field of a workflow step, editors (such as VS Code) may offer a preview of the file. If you take the first few lines of the CWL to write up a synopsis of what the CWL does, this will then be shown on hover.

Autocomplete for the run field is a file picker

Typing in the run field of a step triggers an inline file picker. Typing . will offer all CWL files and all sub-directories relative to the current file. Typing .. will offer all CWL files and sub-directories one level up, and so on.

Go to definition for run field

Employing the "go to definition" action on the run field will open the linked CWL it refers to.

Configuration

The configuration file is found under $XDG_CONFIG_HOME/sevenbridges/benten/config.ini (If $XDG_CONFIG_HOME is not set, $HOME/.config/sevenbridges/benten/ is used)

On first startup benten will create a default configuration file for you. The configuration file is in the .ini format and is fairly self-explanatory. The default file can be found here

CWL language versions

The language model is created directly from the language specification. The specification is found under $XDG_CONFIG_HOME/sevenbridges/benten/ and is named after the CWL version, such as schema-v1.0.json etc. The cwlVersion tag in the document is used to infer which language specification needs to be used. If no cwlVersion is found the latest released specification is used.

The schema-X.json files are created using the schema-salad-tool using the --print-avro option e.g.

schema-salad-tool --print-avro ~/path/to/cwl/schemas/CommonWorkflowLanguage.yml > schema.json

Reporting bugs

Log files are found under $XDG_DATA_HOME/sevenbridges/benten/logs (If $XDG_DATA_HOME is not set, $HOME/.local/share/sevenbridges/benten/logs is used). The log from the current run is benten-ls.log. Logs from previous runs are preserved in a rotating fashion. These logs could be attached to bug reports as needed. They do contain file names and paths.