Workflow Elements

This section contains a detailed description of all workflow elements presented in the Workflow Designer.

For each element, you can find:

  • Description of the parameters used in the GUI.
  • Corresponding parameter names used in a workflow file.
  • Information about input and output ports.

The type of a parameter can be one of the following:

string

A string.

numeric

A number.

boolean

A boolean data type. Available values are: true/false, 0/1, and yes/no.

A port’s slot type can be one of the following:

sequence

Biological sequence

msa

Multiple sequence alignment

text

A text

annotation-table

Table of annotations

annotation-table-list

A list of different tables of annotations

ebwt-index

Bowtie index

hmm2-profile

An HMM profile of the HMMER2 package

fmatrix

Frequency matrix

wmatrix

Weight matrix

sitecon-model

SITECON model

assembly

Assembly

variation

Variation track

To search for an element, use the name filter or press the Ctrl+F shortcut, which moves you to the name filter also:

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