Tools

Data Management This task should be performed in the Data Management section.

In this section, you will learn how to create, manage, and assign Analysis Tools to specific workflows within the COHESIVE system. Tools represent the software or bioinformatics methods used to process data, such as sequencing data, and they are integral components of the analysis pipeline.

Accessing the Tools Section

You can access the List of Analysis Tools section in the following ways:

1. Direct Link:
   You can navigate directly to the Tools management page by using the following link:
   <http://your_instance:your_port/cmdbuild/ui/#classes/T_ESAME_METODO/cards>

2. Navigation Menu:
   You can also access the Tools section via the main menu:
   Data Management → Others → List of Analysis Tools

This will open the page where you can create, edit, and manage different tools used in the system.

Adding a New Tool

To create a new analysis tool, follow these steps:

1. Click on "Add card":
   In the top left corner of the List of Analysis Tools page, click the Add card button.

2. Fill in the Details: You will be presented with the following fields to complete:

   • Code: Enter a unique code to identify the tool (e.g., tool_1).
   • Source: Select the relevant Source associated with this tool (e.g., BIOINFONAS).
   • Description: Provide a brief description of the tool (e.g., "Tool 1").
   • Files RGXP: Ignore this field.
   • Input RGXP: Ignore this field.
   • Notes: Add any additional notes or details that are useful for future reference (optional).

3. Save the Tool: After filling in all required fields, click Save to create the new tool. Alternatively, click Save and close to create the tool and return to the main page.

Why Tools Are Important

Tools are an essential part of the Cohesive system as they represent the various software methods applied in data analysis workflows. Assigning specific tools to workflows ensures that the correct bioinformatics methods are used in each analysis step. Tools can represent anything from basic trimming tools to complex genome assembly or variant calling methods.

Example: Tool Creation

Tool 1:

• Code: tool_1
• Source: BIOINFONAS
• Description: "Tool 1"
• Files RGXP: (leave blank)
• Input RGXP: (leave blank)
• Notes: "My first tool"

Tool 2 Version 1:

• Code: tool_2_ver1
• Source: BIOINFONAS
• Description: "Tool 2 Version 1"
• Files RGXP: (leave blank)
• Input RGXP: (leave blank)
• Notes: "My second tool"

Tool 2 Version 2:

• Code: tool_2_ver2
• Source: BIOINFONAS
• Description: "Tool 2 Version 2"
• Files RGXP: (leave blank)
• Input RGXP: (leave blank)
• Notes: "My third tool"

Managing and Linking Tools

Tools are not standalone entities. They are usually linked to Analysis Types and Steps in workflows. Once a tool is created, it can be assigned to a specific step in the workflow, ensuring that the correct tool is used at the right time. This structure is vital for ensuring reproducibility and consistency in analysis pipelines.

• Tools can be reused across different workflows.
• Multiple versions of a tool can be created (e.g., tool_2_ver1, tool_2_ver2) to support various analysis options.
• Tool execution is automated through Nextflow scripts as part of the analysis steps.

Workflow Integration

The tools created here will be used in various analysis pipelines. Once a tool is defined, it will be associated with a specific Step in the pipeline, ensuring that the correct method is executed as part of the analysis.

• Step 1 may use tool_1 to preprocess raw sequencing data.
• Step 2 may use tool_2_ver1 or tool_2_ver2 to assemble the processed data, depending on the user’s choice.

Each tool can be linked to multiple steps, and new tools can be added as needed to accommodate the ever-evolving needs of bioinformatics workflows.

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By managing tools efficiently, the Cohesive platform ensures a structured and flexible analysis pipeline, allowing users to tailor their workflows to specific needs.