Steps

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

In this section, we will go over how to create and manage Steps within the system. Steps represent individual processes or actions in a workflow and are defined using Nextflow scripts. Each step corresponds to a specific tool and can process data through a sequence of operations.

Adding a New Step

To create a new step, follow these steps:

1. Click on "Add card":
   In the top left corner of the Steps 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 identifier for the step (e.g., step_1).
   • Description: Provide a brief description of the step (e.g., Step_1).
   • json_params: You can leave this field blank for now.
   • script: Define the Nextflow script that will be used to process this step (e.g., tool_1.nf).
   • multi_sample_input: If this step handles multiple samples, check this box. Otherwise, leave it unchecked.
   • Analysis: Select the relevant analysis type for this step (e.g., "Analysis 1" previously created in Analysis Types).
   • Method: Select the corresponding tool for this step (e.g., Tool 1 previously created in Tools).
   • Importable: Ensure this is checked to allow data import for this step.

3. Save the Step:
   After filling in all required fields, click Save or Save and close to create the new step.

Setting Up Input, Output, and Results

1. Use Inputs of Type:

   • Result Types: This field specifies the type of input data required by this step. For example, if your step requires FASTQ files as input, you would select fastq as the input type.
   • Example: For Step 1, select fastq (Raw reads - fastq) as the input type.

2. Produces Output of Type:

   • Result Types: This field defines the type of output that this step will produce. For example, if your step generates output in a custom format like tool1, you would specify tool1 here (previously created in Tools)
   • Example: For Step 1, select tool1 as the output type.

3. Results Template:

   • This field links the step to a specific results template, which defines how the results will be displayed in the system. You can choose a default template or create a custom one.
   • Example: You can leave this set to default if no custom results template is needed.

Example Steps

Example 1: Step 1 - Using Tool 1

1. Code: step_1
2. Description: Step 1
3. Script: tool_1.nf
4. Analysis: Analysis 1
5. Method: Tool 1
6. Importable: Checked
7. Use Inputs of Type: fastq
8. Produces Output of Type: tool1
9. Results Template: default

Example 2: Step 2 - Using Tool 2 Version 1

1. Code: step_2_ver_1
2. Description: Step 2 Version 1
3. Script: tool_2_ver_1.nf
4. Analysis: Analysis 2
5. Method: Tool 2 Ver 1
6. Importable: Checked
7. Use Inputs of Type: tool1
8. Produces Output of Type: tool2_ver1
9. Results Template: default

Exercise: Creating Step 2 Version 2

1. Code: step_2_ver_2
2. Description: Step 2 Version 2
3. Script: tool_2_ver_2.nf
4. Analysis: Analysis 2
5. Method: Tool 2 Ver 2
6. Importable: Checked
7. Use Inputs of Type: tool1
8. Produces Output of Type: tool2_ver2
9. Results Template: default

Exercise

Finish to set-up appropriately all the steps in according to previously created Analysis-Types and Tools.