Arguments

All the BioExcel building blocks are wrappers of tools that accept one or more input file paths as inputs, one or more output file paths as outputs and, optionally, several properties to customize the execution of the wrapped tool.

Inputs

It’s mandatory to pass at least one input file path in string format. Inputs can be required or optional (but as said before, at least one must be required).

In the biobb_template example there are two inputs:

input_file_path1: Defined as required. String with the path of the file.
input_file_path2: Defined as optional. String with the path of the file.

A config file with the properties could also be considered as an input file, but as described below, the properties can be passed to a BioBB in several different ways.

Outputs

It’s mandatory to pass at least one output file path in string format. Outputs can be required or optional (but as said before, at least one must be required).

In the biobb_template example there is one output:

output_file_path: Defined as required. String with the path of the file.

Properties

What are the properties?

BioExcel Building Blocks are wrappers of third-party tools. Most of these tools need specific parameters in order to be executed properly. For this purpose, BioBBs provide the ability of passing specific properties to each tool. In the biobb_template example several properties are sent to the tool, and the definition of each of these properties is explained in detail in this same section.

Pass properties to BioBBs

Properties can be passed to a BioBB in different ways:

As a file

Creating a config file that will be passed to the Python class as an input file path in a command line call. Accepted formats:

YAML

template --config template.yml --input_file_path1 input1 --input_file_path2 input2 --output_file_path output

JSON

template --config template.json --input_file_path1 input1 --input_file_path2 input2 --output_file_path output

As a string

In case we launch a BioBB through command line, we can also pass the properties in a string in JSON format.

template --config '{"boolean_property":false}' --input_file_path1 input1 --input_file_path2 input2 --output_file_path output

As a Python dictionary

Properties can also be passed to the Python class as a Python dictionary directly to the properties argument of the Python class.

prop = {
    "boolean_property": False
}
template(input_file_path1=input1, 
         output_file_path=output, 
         input_file_path2=input2, 
         properties=prop)

In the biobb_template example there are two wrappers:

template.py: Wrapper for the zip tool.
template_container.py: Wrapper for the zip tool executed through a container.

The properties for both examples are different since the execution of tools through container need specific properties.

Template class

Below there is the dictionary of properties for the template.py tool:

boolean_property (bool) - (True) Example of boolean property.
binary_path (str) - (”zip”) Example of executable binary property.
remove_tmp (bool) - (True) [WF property] Remove temporal files.
restart (bool) - (False) [WF property] Do not execute if output files exist.

There are two types of properties in this template:

Specific properties for this BioBB

boolean_property (bool): is a property defined specifically for this BioBB as an example of specific property. There are several data types that can be used: boolean (bool), integer (int), float (float), string (str) and dictionary (dic). In the biobb_template example, this property enables / disables the verbose (-v) operation.
binary_path (str): is used to define the path of the binary wrapped by the BioBB. Usually in case the user doesn’t want to execute the default binary provided by the environment.

Properties common in all BioBB

can_write_console_log (bool): Output log to console.
global_log (Logger object): Log from the main workflow. Workflow property.
prefix (str): Prefix if provided.
step (str): Step indentifier in a workflow. Workflow property.
path (str): Absolute path to the step working dir. Workflow property.
remove_tmp (bool): Remove temporal files. Workflow property.
restart (bool): Restart from previous execution. Workflow property.

As we can see, not all of these properties are defined in the template.py tool. If they are not defined, the system assigns default values to them.

TemplateContainer class

Below there is the dictionary of properties for the template_container.py tool:

boolean_property (bool) - (True) Example of boolean property.
binary_path (str) - (”zip”) Example of executable binary property.
remove_tmp (bool) - (True) [WF property] Remove temporal files.
restart (bool) - (False) [WF property] Do not execute if output files exist.
container_path (str) - (None) Container path definition.
container_image (str) - (’mmbirb/zip:latest’) Container image definition.
container_volume_path (str) - (’/tmp’) Container volume path definition.
container_working_dir (str) - (None) Container working directory definition.
container_user_id (str) - (None) Container user_id definition.
container_shell_path (str) - (’/bin/bash’) Path to default shell inside the container.

There are three types of properties in this template:

Specific properties for this BioBB

boolean_property (bool): is a property defined specifically for this BioBB as an example of specific property. There are several data types that can be used: boolean (bool), integer (int), float (float), string (str) and dictionary (dic). In the biobb_template example, this property enables / disables the verbose (-v) operation.
binary_path (str): is used to define the path of the binary wrapped by the BioBB. Usually in case the user doesn’t want to execute the default binary provided by the environment.

Container specific properties

container_path (str): Container path definition (docker / singularity).
container_image (str): Container image definition (image indentifier for docker, path to image for singularity).
container_volume_path (str): Container volume path definition. Path inside the container where the temporary files created by the wrapper will be mapped.
container_working_dir (str): Container working directory definition. path inside the container where the job will be executed.
container_user_id (str): Container user_id definition.
container_shell_path (str): Path to default shell inside the container.

Properties common in all BioBB

can_write_console_log (bool): Output log to console.
global_log (Logger object): Log from the main workflow. Workflow property.
prefix (str): Prefix if provided.
step (str): Step indentifier in a workflow. Workflow property.
path (str): Absolute path to the step working dir. Workflow property.
remove_tmp (bool): Remove temporal files. Workflow property.
restart (bool): Restart from previous execution. Workflow property.

As we can see, not all of these properties are defined in the template_container.py tool. If they are not defined, the system assigns default values to them.