Selectors and StringFormatting¶

Methods to reference or transform inputs

Overview¶

A janis.Selector is an abstract class that allows a workflow author to reference or transform a value. There are 3 main forms of selectors:

janis.InputSelector - Used for selecting inputs
janis.WildcardSelector - Used for collecting outputs
janis.StringFormatter - Constructing or transforming strings

InputSelector¶

Declaration¶

class janis.InputSelector(input_to_select, remove_file_extension=None, type_hint=<class 'janis_core.types.common_data_types.File'>, **kwargs)[source]¶

Overview¶

An InputSelector is used to get the value of an input at runtime. This has a number of use cases:

Collecting outputs through the glob= field.
Constructing a janis.StringFormatter from existing inputs

These inputs are checked for validity at runtime. In CWL, defaults are propagated by definition in the language spec, in WDL this propagation is handled by janis.

Example¶

The following code will use the value of the outputFilename to find the corresponding output to bamOutput. Additionally as the data_type BamBai has a secondary file, in WDL janis will automatically construct a second output corresponding to the .bai secondary (called bamOutput_bai and modify the contents of the InputSelector to correctly glob this index file.

def outputs(self):
    return [
        ToolOutput("bamOutput", BamBai, glob=InputSelector("outputFilename"))
    ]

WildcardSelector¶

Declaration¶

class janis.WildcardSelector(wildcard, select_first=False)[source]¶

Overview¶

A wildcard selector is used to glob a collection of files for an output where an InputSelector is not appropriate. Note that if an * (asterisk | star) bind is used to collect files, the output type should be an array.

Example¶

The following example will demonstrate how to get all the files ending on .csv within the execution directory.

def outputs(self):
    return [
        ToolOutput("metrics", Array(Csv), glob=WildcardSelector("*.csv"))
    ]

StringFormatting¶

Declaration¶

class janis.StringFormatter(format: str, **kwargs)[source]¶

Overview¶

A StringFormatter is used to allow inputs or other values to be inserted at runtime into a string template. A StringFormatter can be concatenated with Python strings, another StringFormatter or an InputSelector.

The string "{placeholdername}" can be used within a string format, where placeholdername is a kwarg passed to the StringFormatter with the intended selector or value.

The placeholder names must be valid Python variable names (as they’re passed as kwargs). See the String formatter tests for more examples.

Example¶

Initialisation

StringFormatter("Hello, {name}", name=InputSelector("username"))
Concatenation

"Hello, " + InputSelector("username") InputSelector("greeting") + StringFormatter(", {name}", name=InputSelector("username"))