NextSeq 1.0 Sample Sheet Generation for bcl2fastq v2.15
Package Version: BaseSpace Clarity LIMS NextSeq Package v1.0.1; bcl2fastq v2.15
New in 1.0.1:
| • | Configuration changed to use generate_bcl2fastq_sample_sheet script for sample sheet generation. |
| • | Update to the configuration shown in Script usage to make use of new sample sheet options, such as -useSampleLimsID and -appendLimsID. |
Contents
| • | Overview |
| • | Configured Step UDFs |
| • | Submitted Sample UDFs |
| • | Script Parameters |
| • | Script Usage |
| • | Logging |
| • | Sample Sheet Data |
As a part of the NextSeq integration, BaseSpace Clarity LIMS provides the ability to generate a sample sheet from the Denature, Dilute and Load Sample (NextSeq) 1.0 step.
The sample sheet is generated by means of a script, which is initiated when the user clicks a button on Record Details view.
The generated sample sheet is intended to be used with the bcl2fastq conversion tool, provided by Illumina. The tool handles demultiplexing and conversion of the BCL base-call files output by the NextSeq instrument into FastQ files used by many third-party analysis platforms.
With this package, the LIMS provides support for bcl2fastq v2.15. For more information on this product, see Illumina's bcl2fastq User Guide.
The fields listed in the following table are available on the Denature, Dilute and Load Sample (NextSeq) 1.0 step and will be placed into the sample sheet.
|
Field Name |
Field Type |
Required? |
|
Experiment Name |
Text |
No |
|
Workflow |
Text |
Yes |
|
Read 1 Cycles |
Numeric |
No |
|
Read 2 Cycles |
Numeric |
No |
|
Adapter |
Text |
No Required if using 'Adapter Read 2' |
|
Adapter Read 2 |
Text |
No |
|
Mask Adapter |
Text |
No Required if using 'Mask Adapter Read 2' |
|
Mask Adapter Read 2 |
Text |
No |
|
Field Name |
Field Type |
Required? |
Notes |
|
Description |
Text |
No |
See “-l {useProjectLimsID}” command-line parameter. (Script Parameters section) |
|
-u {username} |
LIMS username (Required) |
|
-p {password} |
LIMS password (Required) |
|
-i {processURI} |
NextSeq sequencing process URI (Required) (lower case I) |
|
-c, {csvFileLimsID} |
Sample Sheet CSV file LIMS ID (Required) |
|
-e, {logFileName} |
Log file name (Required) |
|
-l, {useProjectLimsID} |
Accepted values: true or false. Provide with quotes e.g. -l 'true' (Optional) Project LIMS IDs will be used instead of Project Names in the sample sheet (lower case L) |
|
-s {useSampleLimsID} |
Accepted values: true or false. Provide with quotes e.g. -s 'true' (Optional) Sample LIMS IDs will be used instead of Sample Names in the sample sheet |
|
-a {appendLimsID} |
Accepted values: true or false. Provide with quotes e.g. -a 'true' (Optional) The LIMS ID of the step will be appended to the Sample Name values in the sample sheet. Use this option to guarantee unique FASTQ file names per run. |
Below is the default command line that ships with the Denature, Dilute and Load Sample (NextSeq) 1.0 step in new installations. The generate_bcl2fastq_sample_sheet script portion of the parameter string is shown in bold.
bash -c “/usr/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:setUDF -u {username} -p {password} -i {processURI:v2:http} -f 'Progress' -t '//input/@uri-<//sample/@uri' -v 'Library ready for sequencing' && /usr/bin/java -jar /opt/gls/clarity/extensions/Illumina_NextSeq/v1/EPP/nextseq-extensions.jar script:generate_bcl2fastq_sample_sheet -u {username} -p {password} -i {processURI:v2:http} -c {compoundOutputFileLuid1} -e {compoundOutputFileLuid2} "
|
Info Messages |
Reason/Condition |
|
[Info] – Added data line for input: {sample data added for} |
For each line of data added to the sample sheet. |
|
[Info] - Successfully generated Illumina MiSeq Sample Sheet. Script added {number of lines added} lines to sheet. |
On successful completion with no errors or warnings. |
|
Error Messages |
Reason/Condition |
|
Unable to determine {user or password} . |
Unable to determine FTP credentials for ftp.user or ftp.password. |
|
Workflow is a required Field. |
Workflow is not set. |
|
If you specify Read 2 Cycles, then you must also specify Read 1 Cycles |
Read 2 Cycles is set, but Read 1 Cycles is not set. |
|
If you specify Adapter Read 2, then you must also specify Adapter |
Adapter Read 2 is set, but Adapter is not set. |
|
If you specify Mask Adapter Read 2, then you must also specify Mask Adapter |
Mask Adapter Read 2 is set, but Mask Adapter is not set. |
|
This step only supports a single NextSeq Reagent Cartridge. Please restart the step with a single Cartridge. |
More than one output container was found for the step. |
|
Could not find NextSeq Reagent Cartridge RFID. The protocol step doesn't seem to output the correct type. |
Cannot find NextSeq Cartridge container type associated with the protocol step. |
|
Could not find a file output. Ensure your EPP string is configured with the correct parameters. |
Cannot find a shared result file output whose LIMS ID matches the one provided on the command line for the sample sheet. |
|
All inputs must have a single index. Inputs {name of artifact} has no index. |
Encountered a sample without an index when single index is expected. |
|
All inputs must be dual indexed. Input {name of artifact} has no index. |
Encountered a sample without an index when dual index is expected. |
|
In a non-indexed run there can only be one input. |
Encountered a second sample with no index when the first sample had no index. |
|
Input {name of sample} has an index. Another input was non-indexed. Only one input can be provided on a non-indexed run. On an indexed run, all inputs must be uniquely indexed. |
Encountered a sample with an index after already encountering a sample with no index. |
|
Unable to find reagent type {reagent label} for input {name of artifact}. |
Cannot find a reagentType that matches the label on a sample. |
|
Duplicate index found on input {name of sample}. All inputs must have a unique index. |
Encountered a sample with a duplicate index. |
|
All inputs must have a single index. Input {name of sample} has a dual index. |
Encountered a sample with a dual index when we expect all samples to have a single index. |
|
All inputs must have a dual index. Input {name of sample} has a single index. |
Encountered a sample with a single index when we expect all samples to have a dual index. |
Below is a listing of all fields that can appear in the sample sheet and the fields that are populated.
Only items in bold are used by the bcl2fastq tool when processing. Other fields will be ignored by the tool and are there for your convenience.
|
Field Name |
Required? |
Populated by |
Comments |
|
[Header] |
|||
|
Investigator Name |
No |
LIMS technician name |
|
|
Experiment Name |
No |
Step UDF |
|
|
Date |
No |
EPP run date |
|
|
Workflow |
Yes |
Step UDF |
|
|
[Reads] |
|||
|
Read 1 Cycles |
No |
Step UDF |
|
|
Read 2 Cycles |
No |
Step UDF |
|
|
[Settings] |
|||
|
Adapter |
No* |
Step UDF |
Required if AdapterRead 2 is used. |
|
AdapterRead 2 |
No |
Step UDF |
|
|
MaskAdapter |
No* |
Step UDF |
Required if MaskAdapterRead 2 is used. |
|
MaskAdapterRead 2 |
No |
Step UDF |
|
|
[Data] |
|||
|
SampleID |
No |
Sample LIMS ID |
|
|
SampleName |
No |
Sample Name |
Will be sample name or LIMS ID, depending on command-line value. An additional command line option allows the step LIMS ID to be appended to the end of this value, e.g. "Sample1-1234". (See Script parameters). |
|
SamplePlate |
No |
Sample input plate |
|
|
SampleWell |
No |
Sample input well location |
|
|
index |
No |
Sample reagent label |
Dual index reagents will contain a hyphen-separated DNA sequence. This field will use the first half of that value. |
|
index2 |
No |
Sample secondary reagent label |
Dual index reagents will contain a hyphen-separated DNA sequence. This field will use the second half of that value. |
|
Project |
No |
Sample project Will be name or LIMS ID of the project for the first sample in the sample sheet (see Script parameters). |
|
|
Description |
No |
Sample UDF |
Sample UDF |
