Task templates control the target scanning and genotyping processes for a sample. The results of the genotyping are stored in as result fields and genotyping details in the task entries of the sample.

Each project may have several task templates.

Targets of a task template usually correspond to genes that should be analyzed (but they can also be defined independently of genes).

Managing Task Templates

Managing Task Templates

Select Option | Task Templates to see a table with all Task Templates on the server (that are visible for the current user). Use the three fields to filter the table by a simple text, by the owner of a Task Template, or a project in which it is used.

Depending on the number of selected Task Templates, the following buttons are available right to the table:

• Create New: Open the wizard dialog to create a new Task Template.
• Download: Download Task Templates from the Task Template Sphere.
• Import from File: Import a Task Template from XML file.
• Edit: Edit the currently selected Task Template. Locks it for other users.
• Duplicate: Create a duplicate of the currently selected Task Template.
• Export to File: Export the Task Template into an XML file.
• Delete: Delete the currently selected Task Template.
• View: View the currently selected Task Template.
• Export ref.-seq.s: Export the ref.-seq.s of the currently selected Task Template.

All edits, deletion and creates are not stored until the dialog is confirmed with the Save Changes button.

Creating a New Task Template

Task Template Creation Wizard

If specific genes should be analyzed, it is sometimes necessary to create an own task template. The task template can be created with a wizard dialog.

In the menu bar choose File | New | Task Template.

Different workflows are available for different types of task templates, with the following steps:

• Choose Data Type (Sanger or whole genome sequencing data)
• Choose one of the wizard workflows
  • Create from a predefined MLST scheme
  • Choose genes of a seed genome
  • Create Task Template by Allele Libraries
  • Create an empty Task Template and define everything manually

After choosing a wizard workflow a specific tasktemplate can be created. Further steps may or may not appear, depending on the chosen data type and wizard workflow:

• Define genotyping libraries
• Add example read files to guess file naming conventions
• Control and edit file naming conventions
• Adjusting the target parameters
• Defining access rights and usage in a project

Hint: To create Task Templates for a new cgMLST scheme, use the cgMLST Target Definer. Standardized cgMLST schemes with a global nomenclature can be downloaded from the Task Template Sphere.

Editing a Task Template

Task Template Editor

Editing all targets at the same time

Open Option | Task Templates, choose a Task Template and press the Edit button to open it in the Task Template editor window.

The editor window has five different tabs:

Targets

Shows a table with all targets of this Task Template and allows user to edit, create or delete targets.

Task Procedure

Allows to edit or view the Task Procedure of this Task Template.

File Naming

(only available for Task Templates for Sanger sequencing data)
Allows user to edit the file naming conventions for reads of this Task Template.

Genotyping Libraries

Allows user to edit the genotyping libraries of this Task Template.

Result Fields

Allows user to edit the result fields of this Task Template.

Comments

Genus, Species, Application (e.g., Typing, Resistance, Virulence), PubMed ID and any further comments can be stored here.

Curator

The curators that are responsible for this Task Template.

Attachments

Allows user to edit the attachments of this Task Template.

Editing Task Template Targets

The first tab in the Task Template editor shows a table with all targets that are defined in this Task Template. If the targets were created from a genome sequence, further columns can be shown using the small columns selection button in the upper right corner of the table.

Depending on the number of selected targets, the following buttons are available right to the table:

• Add Target: Add a new target by defining the name and target parameters manually.
• Add from Ref-Genome: Add a new target by extracting it as core gene from a seed genome.
• Import from XML: Import all targets from a previously exported Task Template
• Edit Selected Target/Edit All Targets: Edit the target parameters of selected targets or all targets. The parameters of multiple selected or all targets can be edited simultaneously. In this case only the parameters that are marked (use the checkbox in the tabs) will be changed for the targets.
• Duplicate: Create a duplicate of the currently selected target.
• Delete: Delete the currently selected target. Optionally a deletion reason can be given that will be added to the Task Template comment (e.g., when optimizing a soft defined cgMLST task template).
• Move Up: Move the currently selected target up to change the order of the targets.
• Move Down: Move the currently selected target down to change the order of the targets.
• Sort Alphabetically: Sort the targets by their names.
• Export Table: Export the target table to a file.