first draft connect

Author: aleidel

paper/paper.md

@@ -66,7 +66,8 @@ SciWIn-Client is a command-line application based on Rust that makes it simple t
 
 
 ## Creation of CWL Files
-To create CWL CommandLineTools, users must prefix their tool or script invocations with the `s4n create` prefix. The SciWIn client automatically identifies the inputs of the CommandLineTool based on the program call. Outputs are the newly generated files produced after executing a command or script. When a new project is initialized, a Git repository is created in the background to provide a version-controlled environment for tracking changes and support this process. While the system can automatically infer inputs and outputs, users also have the option to define them explicitly. Users can specify a container image pulled from Docker Hub or provide paths to local Dockerfiles to ensure consistent, reproducible execution environments across different systems.
+To create CWL CommandLineTools, users must prefix their tool or script invocations with the `s4n create` prefix. The SciWIn-Client automatically identifies the inputs of the CommandLineTool based on the program call. Outputs are the newly generated files produced after executing a command or script. When a new project is initialized, a Git repository is created in the background to provide a version-controlled environment for tracking changes and support this process. While the system can automatically infer inputs and outputs, users also have the option to define them explicitly. Users can specify a container image pulled from Docker Hub or provide paths to local Dockerfiles to ensure consistent, reproducible execution environments across different systems.
+Once individual CWL CommandLineTools have been created, the next step is to combine them into a CWL Workflow. This is achieved using the `s4n connect` command, which allows the user to specify a source (starting tool or node) and a target (a subsequent tool or node). By linking the output of one tool to the input of another, the user defines the workflow's execution sequence. For instance, the command `s4n connect --from tool1/output --to tool2/input` establishes a connection from tool1's output to tool2's input.
 
 ## Workflow Execution
 The simplest way to execute a workflow is to run it directly on the machine where the workflow is defined by using the `s4n execute local` command (or `cwltool` which however does not support Windows).