Copy UDFs

Available from: Clarity LIMS v2.0.5.

Often, a user has certain values associated with libraries prior to preparing a flow cell. When loading the libraries into the flow cell, the user needs to track these values as attributes of the flow cell lane to help interpret the metrics generated during sequencing.

For example, one might need to record a concentration as a sample UDF on normalized and pooled libraries. This can be accomplished by copying the value of identically named UDFs from inputs to non-shared outputs.

Script Overview

The copyUDFs script provides the ability to selectively copy the value of an input UDF to a UDF of the same name on outputs generated by a protocol step (process). Other capabilities of this script include:

• The ability to map a single input to one or more outputs

• The ability to define which UDF is copied across to outputs

Script Parameters

Parameter	Description
-u {username}	(Required) LIMS login username
-p {password}	(Required) LIMS login password
-i {processURI:v2}	(Required) LIMS process URI
-f {name, name, name}	(Required) UDF names (Required)

Command Line Example

Example

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
    script:copyUDFs \
        -u {username} \
        -p {password} \
        -i {processURI:v2} \
        -f 'myUDF1,myUDF2,myUDF3'"

ℹ️ In the example shown above, the paths may differ for your system. For example, the version number may differ.

Constraints

• Only the UDFs named in the -f (fields) parameter will be copied.

• If input UDFs are not defined or have no value, nothing will be copied for those UDFs.

• UDFs not being defined on an output result in the script aborting after displaying an error message.

• The script is not applicable to shared outputs.

• UDFs of the same name must be present in the input and enabled as an output detail.