Branching elements
Branching elements control the path that data takes through a workflow based on aspects of the data.
Branch on Sequence Count
Branch on Sequence Count (
) elements are used when downstream handling of sequence lists should depend on the
number of sequences in the list.
The sequence list provided as input will flow through the Pass or the Fail output channel depending on whether the number of sequences meets the condition specified in the branching element (figure 14.52).
Figure 14.52: If the sequence list provided as input meets the condition specified in a Branch on Sequence Count element, it will flow through the Pass output channel and be used in the Assemble Sequences step. Otherwise, it will flow through the Fail output channel, where here, it would not be processed further.
In the Branch on Sequence Count configuration dialog (figure 14.53), the configuration options are:
- Comparison The operator to use for the comparison:
>=,=or<=, offered in a drop-down list. - Number of sequences The number of sequences to use in the comparison.
Figure 14.53: Configuration of a Branch on Sequence Count element
Branch on Coverage
Branch on Coverage (
) elements are used when downstream handling of read mappings should depend on whether coverage in that mapping meets a specified threshold. A read mapping and a corresponding report containing coverage information are supplied as input. The read mapping flows through the Pass or the Fail output channel depending on whether or not the coverage level in the report meets the condition specified in the branching element (figure 14.54).
Reports generated by the following tools are supported for use with Branch on Coverage elements:
- QC for Targeted Sequencing
- QC for Read Mapping Note: Zero coverage regions in these reports are ignored.
Figure 14.54: A read mapping and a report flow into the Branch on Coverage element. If the coverage according to the report meets the condition configured in the branching element, the mapping will flow through the Pass output channel and be used in the Basic Variant Detection step. Otherwise, it will flow through the Fail channel, where here, it would not be processed further.
In the Branch on Coverage configuration dialog (figure 14.53), the configuration options are:
- Type The type of coverage value,
Minimum,Median,AverageorMaximum, offered in a drop-down list. - Comparison The operator to use for the comparison:
>=,=or<=, offered in a drop-down list. - Value The coverage value for the comparison.
Figure 14.55: Configuration of a Branch on Coverage element
Branch on Sample Quality
Branch on Sample Quality (
) elements are used where downstream handling of data should depend on quality aspects of that data. Quality information is read from a corresponding sample report or combined report. Based on that information, the input data flows out of the branching element into one of three downstream workflow paths (figure 14.56).
The flexibility of the Branch on Sample Quality element is due to its dependence on information in the "Quality control" subsection of sample reports. The information in that subsection is configured in Create Sample Report (see Create Sample Report). Combine Reports containing sample reports with quality information can also be used as input to the Branch on Sample Quality element (see Combine Reports).
Figure 14.56: Branch on Sample Quality has an input channel for the data and an input channel for a corresponding report containing quality information. Data flows through the Passed, Uncertain, or Failed output channel, depending on quality information in the report.
For each quality condition configured in the Create Sample Report tool, a color, yellow or red, can be specified to be assigned when the condition is not met. This information is then used by this branching element as follows:
- If a condition assigned red is not met, the data flows through the Failed channel. Where all such conditions are met, then:
- If a condition assigned yellow is not met, the data flows through the Uncertain channel. Where all such conditions are met, then:
- The data element flows through the Passed channel.
Consequently, if a report without a "Quality control" section is provided, the data element will flow through this channel.
The branching elements Branch on Coverage and Branch on Sequence Count also control the flow of data through a workflow based on quality measures, but they do not have the flexibility of the Branch on Sample Quality element. Specifically, they allow a single quality condition to be specified for a single data type, with data flowing into one of two downstream paths through the workflow.