Modeling Steps

In this example, we will create two steps based on two tools:

1. tool_1
2. tool_2

However, we will imagine that tool_2 has two versions:

• tool_2_ver1
• tool_2_ver2

As a result, we will create three tools and two steps. The first step will use tool_1, while the second step will use both tool_2_ver1 and tool_2_ver2. The input for tool_1 will be raw reads (FASTQ files), and the output generated by step_1 will serve as the input for step_2, which can use either tool_2_ver1 or tool_2_ver2.

Step 1: Using tool_1

1. Tool Description:

   • tool_1 is the first tool in the workflow and will be used for processing raw reads (FASTQ files).

2. Input:

   • The input for tool_1 will be raw sequencing reads in the form of FASTQ files.

3. Output:

   • step_1 will produce output files with the .tool1 extension.

4. Step Definition:

   • A Nextflow script will be created for tool_1 in the steps/ directory.
   • Example filename: step_tool_1.nf
   • This script will define how tool_1 processes the raw reads.

5. Associated Analysis:

   • A new analysis will be created and associated with this step, which will be visible in the Menu under the relevant analysis type.

Step 2: Using tool_2 with Multiple Versions

1. Tool Description:

   • tool_2 is used in the second step of the workflow, and it has two versions: tool_2_ver1 and tool_2_ver2. The user can choose either version depending on the requirements.

2. Input:

   • The input for tool_2 (both versions) will be the output generated from step_1 (i.e., the files with the .tool1 extension).

3. Output:

   • step_2 will produce output files with the .tool2 extension.

4. Step Definition:

   • A Nextflow script will be created for each version of tool_2 in the steps/ directory.
   • Example filenames:
     • step_tool_2_ver1.nf
     • step_tool_2_ver2.nf
   • These scripts will define how tool_2_ver1 and tool_2_ver2 process the input from step_1 and generate the final output.

5. Associated Analysis:

   • A new analysis will be created for both versions of tool_2 and linked to the Menu under the appropriate analysis category. Each version of the tool will have its own entry in the menu, allowing users to select the appropriate tool for their workflow.

Workflow Summary

1. Step 1:

   • Tool: tool_1
   • Input: Raw reads (FASTQ files)
   • Output: Processed files with .tool1 extension
   • Analysis: Associated with a menu item in the system

2. Step 2:

   • Tool: tool_2_ver1 or tool_2_ver2
   • Input: Processed files from step_1 (with .tool1 extension)
   • Output: Final processed files with .tool2 extension
   • Analysis: Associated with menu items for tool_2_ver1 and tool_2_ver2

By structuring the workflow in this way, you can manage different tools and tool versions efficiently. The steps and Nextflow scripts are organized logically in the steps/ directory, following the naming convention described in the Steps and Module page.

Linking Analyses to the Menu

Once the steps and corresponding Nextflow scripts are created, you will need to associate the analyses with the Menu. This can be done by linking each analysis to a specific menu item, ensuring that users can access and run the analyses from the system’s user interface.