Creating and editing Workﬂows

To create or edit a workﬂow, go to Manage Workﬂows... under the Workﬂows menu. Here you have the option to create a New Workﬂow, View/Edit an existing Workﬂow, or Copy and edit an existing Workﬂow. Each of these options opens an Edit Workﬂow window (See example in Figure 17.2 ) 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.

Each Workﬂow is made up of one or more Steps. A Step may be an Operation (for example, perform Muscle alignment), or a special Step (for example, Group Documents). 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. All documents selected when the Workﬂow is run are provided as input to the ﬁrst Step (unless speciﬁed otherwise, see section 17.2.2 for further information). The output from the ﬁnal Step of a Workﬂow is saved in your Geneious database. Outputs from intermediate steps are not saved, unless you include the Save Documents / Branch option after the Step. A document is a single entry that can be selected from your Geneious database. For example a single document can be an alignment, a sequence list, a tree, or a stand-alone sequence.

The Add Step button (Figure 17.3 ) provides a dropdown menu with a range of Steps that can be added to your WorkFlow. The purpose/function of each type of Step is summarised in Table 17.1 .

Table 17.1: Add Step options for Workﬂows


Step	Purpose/Function


Add Operation	Runs one of the standard Operations available in Geneious. This can include other Workﬂows



For Each Document	Runs the next Step in the Workﬂow independently on each document

For Each Sequence/Extract Sequences From List	Runs the next Step in the Workﬂow independently on each sequence, extracting sequences from a list if necessary

Group Documents	Groups results from multiple operations together so that they are all used in a single invocation of the next operation

Group Sequences	Groups sequences into a sequence list document



Add document chosen when running workﬂow	Prompts the user to choose a document when they ﬁrst start the Workﬂow. This document may either be chosen from anywhere in their database, or from one of the documents selected when the workﬂow is run. In the latter case, the selected document will be excluded from the list of documents provided to the ﬁrst Step of the Workﬂow. If only a single document from the selected documents matches the speciﬁed document type, then it will be automatically selected instead of asking the user. In both cases, the selected document is combined with each of the results from the previous Step in the Workﬂow. See section 17.2.2 for more details

Combine with Earlier Document(s)	For each result from the previous Operation, combines with the corresponding input document(s) of an earlier operation in the Workﬂow. The documents from the earlier Operation are added to the end of the list of documents from the previous operation

Save Documents / Branch	Optionally saves the current results. Also, optionally starts a branch beginning from an earlier Step in the Workﬂow



Rename Documents	Renames the document(s)

Copy Property Between Documents	Works on a pair of documents. Copies a property from one document to another document and outputs just the destination document. If only a single document is provided, outputs that document unmodiﬁed

Filter Documents	Filters some documents based on the content of their ﬁelds

Sort Documents	Sorts some documents based on the contents of their ﬁelds



Custom Java Code	Write some custom Java code to do whatever you want. See section 17.3 for more details

17.2 Creating and editing Workﬂows