This document may either be chosen from anywhere in their database, or from one of the documents selected when the workflow is run. Group Sequences: Groups sequences into a sequence list document.Īdd document chosen when running workflow: Prompts the user to choose a document when they first start the Workflow. Group Documents: Groups results from multiple operations together so that they are all used in a single invocation of the next operation. This can include other Workflows.įor Each Document: Runs the next Step in the Workflow independently on each document.įor Each Sequence/Extract Sequences From List: Runs the next Step in the Workflow independently on each sequence, extracting sequences from a list if necessary. The purpose/function of each type of Step is summarised in below:Īdd Operation: Runs one of the standard Operations available in Geneious. The Add Step button provides a dropdown menu with a range of Steps that can be added to your WorkFlow. For example a single document can be an alignment, a sequence list, a tree, or a stand-alone sequence. A document is a single entry that can be selected from your Geneious database. Outputs from intermediate steps are not saved, unless you include the Save Documents / Branch option after the Step.
The output from the final Step of a Workflow is saved in your Geneious database. All documents selected when the Workflow is run are provided as input to the first Step (unless specified otherwise, see Advanced Document Management for further information). Each Step accepts one or more documents as input and produces one or more documents as output which are then used as input to the next step in the Workflow. A Step may be an Operation (for example, perform Muscle alignment), or a special Step (for example, Group Documents). Each of these options opens an Edit Workflow window where you can name your Workflow, describe its function, specify an icon for display in the Workflows menu, share via a Shared database, and build/edit your Workflow using the Add Step/ Delete Step buttons.Įach Workflow is made up of one or more Steps. Here you have the option to create a New Workflow, View/Edit an existing Workflow, or Copy and edit an existing Workflow. To create or edit a workflow, go to Manage Workflows. However, you can use the Copy button to create your own personal editable copy of any Workflow. Workflows shared by other users in a shared database are only editable by the creator. These Workflows will not appear in the drop down menu unless you choose to show them. Workflows shared by other users in a server database are indicated by an icon. Multiple workflows can be selected using Shift- or CNTRL-click, and they can then be exported or added/removed from the drop-down list in one go. The order in which workflows appear in the drop down menu can be altered either by dragging and dropping workflows in the list to their desired position, or by using the Move Up and Move Down buttons. Each workflow listed in the Manage Workflows window with an icon next to it will be shown in the drop down under the main Workflows menu. window lists all available workflows and contains options for viewing, editing, copying, deleting, exporting and importing workflows. The Workflows menu allows you to select and run saved Workflows, manage your Workflows and create new ones. If the Workflows icon does not appear in your toolbar, you can add it by right clicking on the main Geneious Toolbar, choosing Customize.
Workflows can be accessed from the Workflows menu under Tools, or from the Workflows icon in the Geneious Toolbar.
#GENEIOUS PRIME VERSUS R11 CODE#
If you have any programming knowledge you can even add customised code in Java (see Custom code in workflows) Managing Workflows Workflows can be shared with other people either by exporting and importing them, or if you are connected to a shared database, by ticking the option to share them (see below). Workflows can be run or managed via the Tools menu or the Geneious Toolbar.
Geneious Prime provides a number of example Workflows for a variety of tasks that you can try. Options for each Operation may be preconfigured, or some or all options 'exposed' for configuration when the Workflow is run. Workflows allow you to group Operations together to reduce the number of steps required to perform an often-used combination of Operations.
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