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Last Updated: November 2024
Release Date: September 2023
Document Version: 2
These release notes detail the key changes to software components for the Next Generation Sequencing (NGS) Extensions Package v5.23.0.
Refer to Compatibility under Instruments & Integrations.
Updates Java and third-party dependency libraries.
Updates Groovy to v3.0.7.
Stopwatch parameter -s is replaced with the -stopwatch parameter for NGS 5.21.0 and later.
The sample sheet for the MiSeq now shows the following information:
The pool name instead of the sample name when the pool contains only one sample.
The well and plate information for submitted samples instead of for libraries.
Fixed issue where the template file generator created duplicate lines for the first data source entry when using multiple data sources.
Fixed issue where the driver file generator did not append the existing log file.
The changeWorkflow script on the No Output step reflects the correct number of samples being routed.
Fixed the Insecure Input Validation (SRCCLR-SID-22742) vulnerability.
Fixed degradation of the LLTK script performance when updating the custom field with an empty string.
Fixed degradation of the log file download performance when automation performs write actions on an existing log file.
Improved the LLTK script error messages to show details of artifacts.
An error occurs when reformatting the date using the Lab Logic Toolkit with the Date utility class. The date reformatting can be done with java.time instead.
Version
Changes
2
Updated Compatibility section to reference Compatibility matrix table.
1
Initial release.
The Illumina Preconfigured Workflows Package (PCWP) supports the integration of Clarity LIMS with established lab protocols. The integration provides preconfigured workflows that map to lab protocols and steps, and support Illumina library prep kits, reagent kits, and controls. For detailed information on the installed workflows, see the instrument integrations and protocols documentation.
Last Updated: November 2024
Release Date: February 2024
Document Version: 2
These release notes detail the key changes to software components for the Next Generation Sequencing (NGS) Extensions Package v5.24.0.
Refer to under Instruments & Integrations.
Added the following scripts:
validate_selected_container
validate_same_udf_valuee_for_analytes
None
An error occurs when reformatting the date using the Lab Logic Toolkit with the Date utility class. The date reformatting can be done with java.time instead.
The -s in the stopwatch parameter is replaced with -stopwatch in NGS v5.21 and later.
Version
Changes
2
Updated Compatibility section to reference Compatibility matrix table.
1
Initial release.
Last Updated: November 2024
Release Date: June 2024
Document Version: 2
These release notes detail the key changes to software components for the Next Generation Sequencing (NGS) Extensions Package v5.25.0.
Refer to Compatibility under Instruments & Integrations.
Added the download_attachments script. This script copies one or more result files attached in a step to a user-specified directory within Clarity LIMS. For example, this script can copy a generated sample sheet to a mounted directory so that the user can access it directly from the instrument control software.
None
An error occurs when reformatting the date using the Lab Logic Toolkit with the Date utility class. The date reformatting can be done with java.time instead.
Version
Changes
2
Updated Compatibility section to reference Compatibility matrix table.
1
Initial release.
The Clarity LIMS NGS Extensions Package includes the AccessionReagentKitLots script, which automates the accessioning of reagent lots based on container names. This section provides details on the script and its parameters, and LIMS configuration requirements.
Designed for use in automated workflows, the AccessionReagentKitLots creates a new reagent lot, matching the Reagent Kit Name specified in the command line to a reagent kit configured in the LIMS.
The script populates the lot details according to the following logic (see Script Parameters section for details):
Lot Name = Lot name (specified by lotName parameter)
Lot Number = Container name (specified by from parameter)
Expires = now + expiry days (specified by expiryDays parameter)
Status of Reagent Lot toggle switch is set to Active
Before accessioning the reagent lot, the script verifies that:
The expiryDays parameter value is greater than 0, and is a whole number
The reagent lot does not already exist in the LIMS - lots are not reusable.
The script checks whether there is an existing reagent lot in the LIMS that matches the combination of lot name + lot number provided. If so, validation fails. (Kit name is not checked during this validation process.)
If a unique combination of lot name + lot number is provided, the LIMS creates the new lot—even if there are already lots in the LIMS matching either the name or the number.
Note that it is therefore possible to create both of these lots:
Lot 'ABC' with number '123'
Lot 'ABD' with number '123'
Parameter
Description
-u {username} -username {username}
(Required) LIMS login username
-p {password} -password {password}
(Required) LIMS login password
-i {stepURI:v2} -stepURI {stepURI:v2}
(Required) LIMS step URI
-log {logFileLIMSID} -logFileName {logFileLIMSID}
(Required) LIMS ID of the log file placeholder
-from <outputContainer / inputContainer>
-reagentKit <Reagent Kit Name>
(Required) Reagent Kit name on which the generated lot is based.
-lotName <Reagent Lot Name>
(Required) Reagent Lot name to assign to the lot
-expiryDays <#>
(Required) Number of days the lot's expiry date will be set to. Must be greater than zero (script checks for this).
-t <true/false> -testMode <true/false>
(Optional) Runs script in test mode. Script is triggered manually via button on Record Details screen. Defaults to false.
The following sections describe the configuration intended to support the AccessionReagentKitLots script.
Master Step Custom Fields
Configure master step custom fields (step UDFs in v4.x) for reagent kit name and lot name, and display them in the Step Details area of the Record Details screen. When running the step, the user fills in these values and they are supplied to the reagentKit and lotName parameters in the script. In this scenario, configure the automation command line as follows:
Automation trigger
The script is intended to be automatically triggered at the end of a step. However, you may include the -t option to run the script in test mode and trigger the script via button on the Record Details screen.
Reagent Kit Name specified in the command line must match a reagent kit configured in the LIMS.
expiryDays parameter value must meet the following criteria:
Must be a whole number greater than 0.
Must be a numeric value (i.e., '1' not 'one').
When specifying the from parameter, note that the script only supports the value 'outputContainer' if the step outputs are samples. Step output measurement records with placement are not supported.
Accessioning reagent lots with this script sets each reagent lot status to Active until the expiry date is reached. You cannot use the script to add reagent lots with status set to Pending.
The step should only be run with a single container matching the from definition.
If from is defined as the output container, the step can have multiple input containers but all samples must be placed in the same output/destination container. This is because the script only looks up a single container name. If there are multiple output containers in the step, the script will not fail; however, it will choose a container arbitrarily, which could result in unexpected behavior/results.
The Clarity LIMS NGS Extensions Package includes the place_indexes script, which assigns indexes (reagent labels) to samples in the destination container, based on the pattern defined in a specified index pattern file — and optionally validates the indexes against the pattern file.
This section provides details on the script and its parameters, and LIMS configuration requirement
The place_indexes script is intended to be run on entry to, and optionally on exit from, the Add Labels / Reagents screen of a step.
On entry to Add Labels / Reagents screen, the script assignes an index (label) to each sample in the destination container, based on the pattern defined in the specified index pattern file.
On exit from Add Labels / Reagents screen, the script validates the indexes against the pattern file. You can also use the script to check:
If the user has modified the indexes.
If the current step permits user modifications.
The index pattern file is a tab-separated file consisting of two columns, DEST_WELL and INDEX_NAME, and is in the following format:
The destination well format provided in the file must match the well placement configuration of the container type intended for use in the LIMS. The reagent index name must match the name of a reagent in the LIMS.
Pattern name files may be customized. However, for out-of-the-box LIMS integrations, the supplied pattern file names follow the convention: placement_pattern_index_xx_yy.tsv, where:
xx is a short description about the step that accesses this file
yy is a 2-digit value in the range from 01 to 99
There are three levels of validation provided by the script:
Index placement can be modified by the user on the fly.
Index placement is locked down by an administrator and cannot be modified by the user.
Index placement must be locked down by an administrator prior to use.
Two options determine which level of validation to apply:
The presence of a corresponding checksum file for the given pattern file.
The presence of the locked script parameter.
When there is no checksum file, and locked is not provided to the script (or is provided as false), index placement is user-modifiable.
Checksum file
If the reagent index placement pattern is not user-modifiable, an administrator can create a checksum file to ensure that the user has not changed the index placement on the fly.
This checksum file should have the same name as the placement pattern file, but with the file extension .md5. For example:
placement_pattern_index_pcramp_01.tsv
placement_pattern_index_pcramp_01.md5
The checksum file must be placed in the same location as the corresponding index pattern file. When a checksum file is found and the user has modified the indexes on the samples in the step, the script reverses the changes made by the user.
The checksum file contains the .md5 checksum for the corresponding pattern file itself. This checksum value is compared against the pattern file to validate whether the pattern file has been modified. If it has been modified, the script displays an error message and index placement does not occur. If an administrator wishes to change the pattern file contents, they must also regenerate the checksum when the updated pattern is available for use.
Locked patterns
The locked parameter provides an additional layer of validation. If this is provided to the script, the current pattern requires the presence of a checksum file. This ensures that an administrator has approved the pattern for use before it is used in a step.
In some steps where reagent autoplacement is configured, there may be some reagent categories where this is not desired.
For example, the workflow may permit either a full 96 well plate of samples in the indexing step, or merely 8 samples in tubes. For the 8 samples, a different reagent category is used than for the batch of 96. In this case, the ignoredCategory parameter may be used to indicate that if the 8-sample reagent category is selected for the step, index placement will be performed manually.
The place_indexes script is intended to be run on entry to / exit from the Add Labels / Reagents screen of a step.
To achieve this, configure the automation trigger as follows:
Trigger Location: Add Labels screen
Trigger Style: Automatic upon entry / exit
The step must be configured for adding reagent indexes.
The script must run on entry to or exit from the Add Labels / Reagents screen.
The pattern file must be a tab-separated (.tsv) file.
The pattern file headers must be DEST_WELL and INDEX_NAME.
The reagents in the pattern file must match the name of reagents configured in the LIMS.
Only Index type reagents are supported.
The destination container type selected must match the well placement information in the pattern file.
There must not be more samples in the step than are supported by the selected pattern file.
Only a single destination container is supported.
If the locked parameter is provided, a checksum file must be present.
If a checksum file is present, the index placements may not be modified by the user.
The checksum file must be in the same location and have the same name as the pattern file, with extension .md5.
The checksum file contents must be the checksum value for the corresponding pattern file.
If a checksum file is present, the pattern file and checksum file must have the same checksum value.
(Required) Must be either 'outputContainer' or 'inputContainer'. This dictates where the 'Container Name' value is copied from. This is used to create the lot number. Only supports output containers on steps that output samples. See .