2.4 Flow

A flow is assembled from one or more tools. Users may build a flow themselves or subscribe to a community flow and import it into the project. Because jobs run from flows, every analysis must have a flow. A single tool must still be placed in a one-node flow before it can be run as a job; multiple tools can be connected to create a more complex workflow.

Select Flow in the project navigation, then select Create flow.

Create a Flow

The Flow path construction page contains three main components:

• Flow Name: A unique name that does not duplicate another flow in the project.
• Flow path construction: Select a specific tool version from the Tool List on the left, drag it to the canvas, and connect its ports. Use Tool Config to configure selected tools and Format to arrange the canvas.
• Description: A Markdown editor displayed below the flow canvas. The interface describes this area as “Here is the document editing mode of markdown.”


When a tool is placed on the canvas, ports appear on both sides. Ports correspond to input and output files and show the direction in which files move through the flow. Drag an input port to an empty area to expose it as a required flow input. Drag an output port to an empty area to expose it as a final flow output.

A connection from Tool A to Tool B means that Tool A’s output becomes Tool B’s input. The output format from Tool A must satisfy the input-format requirement of Tool B. A connection between two tools transfers the file but does not automatically expose it as a final flow output. To retain that file as a final output, drag an additional line from Tool A’s output port to an empty area of the canvas.

After the graph is assembled, select a tool node and use Tool Config to adjust its parameters and compute resources. Values can be changed according to the tool author’s instructions; otherwise, the default configuration is used. When the Flow Name, Flow path construction, and Description are complete, select Save in the upper-right corner.


Module	Field	Description
Tool information	Top description	Instructions for the tool, including its purpose, usage, and parameter configuration.
Command configuration	CMD	Command line executed when the tool runs. See the tool-development guide for configuration details; users who only run the tool normally do not need to edit this field.
Parameter configuration	param list	List containing tool parameters, input files, and output files.
Parameter configuration	prefix	Whether the parameter uses a command-line prefix. See the tool-development guide; ordinary users normally do not need to edit it.
Parameter configuration	type	Data type: Number, String, Input, or Output.
Parameter configuration	key	Unique parameter identifier. It cannot be duplicated. Tool instructions normally use the key to explain the parameter.
Parameter configuration	value	Configured value. Users may change Number and String values.
Parameter configuration	is select	Whether the parameter is enabled for execution. Required parameters are normally selected by default; optional flags can be enabled or disabled.
File configuration	input/output	The tool input and output files.
File configuration	dir	Subdirectory used for the input or output inside the Docker container. Ordinary users normally do not need to edit it.
File configuration	port	Port name displayed in the flow graph, describing the file accepted or emitted by the port.
File configuration	type	File cardinality. item means one file; array means multiple files can be accepted or emitted.
File configuration	pattern	File-format or suffix restriction. For example, .csv accepts CSV only; a wildcard accepts any format.
Compute resources	Computer selection	Compute resources allocated to the Docker tool.
Compute resources	CPU	Number of CPU cores required.
Compute resources	RAM	Maximum memory available or required.
Compute resources	DISK	Maximum disk storage available or required.

Delete a Flow

Select the flow and choose delete. A flow used by a currently running job cannot be deleted until that job has finished.

Create a Job from a Flow

Select a flow and choose Create Job. The dropdown also provides Create Batch Jobs. Use Search Flows, the refresh icon, pagination controls, or the Go to field to locate other flows.