IGA Library Prep Automated v2.1 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the IGA NovaSeq Sequencing v2.1 workflow and NextSeq 1000/2000 v2.3 workflow (which is installed separately). The protocols provide the following functions:
File-based integration with the Hamilton robots that are used for liquid handling steps.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents.
When required, automatic step transition.
Protocol 1: Sample Selection
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Select Samples
Master Step Name = Select Samples (IGA v2.1)
Step Type = No Outputs
Automations
Validate Sample Attributes (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Sample Selection - Set Library prep method and Next steps (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Sample Selection - Route plated gDNA (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Protocol 2: Sample Plating
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Plate Samples
Master Step Name = Sample Plating (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Variable
Automations
Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)
Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Extraction - Routing (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Step Data (Master Step Fields)
Protocol 5: Illumina DNA PCR-Free
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: DNA Batching PCR-Free
Master Step Name = DNA Batching NFPF (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Placement Reminder (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon entry
DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
DNA Batching PF - Generate LH Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Step Data (Master Step Fields)
Step 2: Index Planning PCR-Free
Master Step Name = Indexing Planning (IGA v2.1)
Step Type = No Outputs
Automations
Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Library Prep - Indexing PCR-Free
Master Step Name = Indexing NFPF (IGA v2.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Automations
Indexing - Validate Index Category and Index Plate Barcode (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v2.1)
Trigger Location = Add Labels
Trigger Style = Automatic upon entry
Library Prep - Indexing PF - Validate/Copy LibPlate Barcode, Set Default Norm. Mol. if Applicable, and Generate LH Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Library Prep - Indexing PF - Check for Valid, Unique LIB Plate Barcode & Match with Liquid Handler Output File & Parse Reagent Info & Set Next Steps to Remove from Workflow & Quant. Warning (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Library Prep - Indexing PF - Route Samples to Sequencing Platform Selection with Automatic Workflow Detection (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Add Labels
Label Groups
Nextera UDP A
Nextera UDP B
Record Details
Step Data (Master Step Fields)
Protocol 6: Illumina DNA with Enrichment
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: DNA Batching with Enrichment
Master Step Name = DNA Batching NFE (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
DNA Batching Enrichment - Set Final Volume (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Placement Reminder (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon entry
DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
DNA Batching Enrichment - Generate LH Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Index Planning with Enrichment
Master Step Name = Indexing Planning (IGA v2.1)
Step Type = No Outputs
Automations
Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Library Prep - Indexing with Enrichment
Master Step Name = Indexing NFE (IGA v2.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Automations
Indexing - Validate Index Category and Index Plate Barcode (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Indexing - Custom Indexing with Hamilton Offsets and Dynamic Index Category Discovery (IGA v2.1)
Capture and Wash Enrichment - Validate LH Output File Name, Parse Reagents & Set Next Steps to Advance (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 6: Post-Capture Pool QC with Enrichment
Master Step Name = Generic Pool QC NFE (IGA v2.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Pool QC - Generic - Enrichment - Copy Normalized Molarity from Output to Input, Copy QC Value to Inputs & Set QC Passed Sample Next Steps to Remove from Workflow (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Pool QC - Generic - Enrichment - Route QC Passed Samples to Sequencing Platform Selection (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Protocol 7: Sequencing Platform Selection
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Select Sequencing Platform
Master Step Name = Sequencing Platform Selection (IGA v2.1)
Step Type = No Outputs
Automations
Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Sequencing Platform Selection - Copy Instrument Type to Analyte & Set Next Steps to Remove from Workflow (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Sequencing Platform Selection - Route to Sequencing Workflow by Type (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Presets
Illumina DNA PCR-Free
Illumina DNA with Enrichment
Quick reference checklist: Sample Selection
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Defaults =
User tasks for this page:
- Select Library Prep Method above
- Select Next Steps
Step File Placeholders
Set Library Prep Method Script Log - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Sample Name
Built-in
Submitted Sample
Naming Convention = {InputItemlName}
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Waiting
Built-in
Expanded View Fields
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Submitted Sample
Library Prep Method
Text
Submitted Sample
Sample Type
Text
Placement Pattern = Column
Destination Containers
96 well plate
Defaults =
User tasks for this page:
- Select blue 'Run' button
- Download Liquid Handler Input File
Quick reference checklist: Sample Plating. ii) post Liquid Handler
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Defaults =
User tasks continued:
- Upload resulting Liquid Handler Output File
- Select Next Steps
Quick reference checklist: DNA Extraction - Blood. i) pre Liquid Handler
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Default =
User tasks for this page:
- Download Liquid Handling Robot Input File
- Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
Quick reference checklist: DNA Extraction - Blood. ii) post Liquid Handler
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Default =
User tasks continued:
- After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File
- Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
Quick reference checklist: DNA Extraction - Saliva. i) pre Liquid Handler
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User tasks for this page:
- Download Liquid Handling Robot Input File
- Enter reagent lots for MLB and ProK (not scanned by Liquid Handler as loaded as a mastermix)
Quick reference checklist: DNA Extraction - Saliva. ii) post Liquid Handler
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Default =
User tasks continued:
- After running Extraction on the liquid handler, upload the resulting Liquid Handling Robot Output File
- Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
Default =
- DNA (ng) required for tagmentation is 300-2000 ng.
- A fixed 25uL is aliquoted from the total volume of 40uL (default) to carry out Library Prep and subsequent steps.
Quick reference checklist: DNA Batching IDPF. i) pre Liquid Handler
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User tasks for this page:
- For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred
- 'Run' DNA Batching PF automation, and download resulting 'Liquid Handler Batching Input File'
Quick reference checklist: DNA Batching IDPF. ii) post Liquid Handler
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User tasks continued:
- Upload resulting 'Output File from Liquid Handler'
- Select 'Next Steps'
Output File from Liquid Handler - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Default = 1
Range From 1 to 12
Quick reference checklist: Indexing Planning
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Default =
User tasks for this page:
- Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column)
- Click 'Next Steps'
Step File Placeholders
Script Log File (Aggregated) - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Naming Convention = {SubmittedSampleName}
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Well
Built-in
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Well
Built-in
Nextera UDP C
Nextera UDP D
Default = CTGTCTCTTATACACATCT
BLT-PF
Text
ELM-T
Text
HP3
Text
Index Plate Barcode (read from input samples)
Text
Read Only
Index Plate Offset (read from input samples)
Text
Read Only
IPB
Text
Library Plate Barcode
Text
Required Field
Liquid Handling Instrument ID
Text
Read Only
Quick reference checklist: Library Prep IDPF. i) pre Liquid Handler
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Default =
User tasks for this page:
- Above, scan in the 'Library Plate Barcode' to be used
- Click blue button to 'Run' the Library Prep automation, and download the resulting 'Liquid Handler Input File'
Quick reference checklist: Library Prep IDPF. ii) post Liquid Handler
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User tasks continued:
- Upload resulting 'Hamilton Output File'
- Perform a pooled quant for the prep, and apply the yield 'Normalized Molarity (nM)' to all samples
- Click 'Next Steps'
Default =
- DNA (ng) required for tagmentation is 50-1000 ng.
- A fixed 30uL is aliquoted from the total volume of 45uL (default) to carry out Library Prep and subsequent steps.
Quick reference checklist i): DNA Batching IDE, pre Liquid Handler
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User tasks for this page:
- For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred
- 'Run' DNA Batching Enrichment automation, and download resulting 'Liquid Handler Batching Input File'
Quick reference checklist ii): DNA Batching IDE, post Liquid Handler
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Default =
User tasks continued:
- Upload resulting 'Output File from Liquid Handler'
- Select 'Next Steps'
Output File from Liquid Handler - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Default = 1
Range From 1 to 12
Quick reference checklist: Indexing Planning
Multiline Text
Read Only
Default =
User tasks for this page:
- Scan in Indexing Plate Barcode and set the Hamilton Indexing Offset column (required start column)
- Click 'Next Steps'
Step File Placeholders
Script Log File (Aggregated) - Manually uploaded
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
Sample Name
Built-in
Derived Sample
Naming Convention = {SubmittedSampleName}
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Nextera UDP C
Nextera UDP D
Quick reference checklist: Library Prep IDE.
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User tasks for this step:
- No user tasks, click 'Next Steps'
Quick reference checklist: Library Prep IDE - pool libraries. i) pre Liquid Handler.
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User tasks for this page:
- 'Run' Library Prep Pooling automation
- Download resulting Liquid Handler Input File
Quick reference checklist: Library Prep IDE - pool libraries. ii) post Liquid Handler.
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User tasks continued:
- After running the Prep method on the Liquid Handler, upload resulting Liquid Handler Output File
- Click on 'Next Steps'
Quick reference checklist: Capture and Wash IDE. i) pre Liquid Handler.
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User tasks for this page:
- 'Run' Capture and Wash automation
- Download resulting Liquid Handler Input File
Quick reference checklist: Capture and Wash IDE. ii) post Liquid Handler.
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Default =
User tasks continued:
- After running Capture and Wash on the liquid handler, upload resulting Liquid Handler Output File
- Click 'Next Steps'
bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-SAM:: ) ) {fail ( ::Invalid SAM Plate Barcode format. This plate ID must be in the format LPxxxxxxx-SAM, where 'x' is a digit 0-9, e.g. LP1234567-SAM. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
bash -l -c "/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/iga_helpers/pop_up_msg.py -s {stepURI} -u {username} -p {password} -w 'OK' --message 'Please place all samples starting from position A:1, do not leave any gaps.'"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-DNA:: ) ) {fail ( ::Invalid DNA plate barcode format. This plate ID must be in the format LPxxxxxxx-DNA, where 'x' is a digit 0-9, e.g. LP1234567-DNA. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI} && \
/usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/validate_sample_placement.py -u {username} -p {password} -s {stepURI}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2:http} \
-u {username} \
-p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (!output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = 0; }; output.::Number of Samples in Pool::++; if (output.::Number of Samples in Pool:: > 12) { fail(::Pools cannot contain more than 12 samples each.::) }' \
-log {compoundOutputFileLuid1}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if ( !output.container.name.matches( ::LP[0-9]{7}-PCPP:: ) ) {fail ( ::Invalid PCPP (Pre-Capture Pool Plate) barcode format. This plate ID must be in the format LPxxxxxxx-PCPP, where 'x' is a digit 0-9, e.g. LP1234567-PCPP. Please verify and try again.:: ) }' -log {compoundOutputFileLuid1} && /usr/bin/env python /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/01_A_CFP_Batching_defaultContainerCheck.py -u {username} -p {password} -s {stepURI}"
IGA NovaSeq Sequencing v2.1 contains preset protocols that support the setup of previously prepared libraries used with the NovaSeq instrument. These protocols can be used with the IGA Library Prep Automated v2.1 workflow. They also provide the following functions:
File-based integration with the Hamilton robots that are used for liquid handling steps.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents.
When required, automatic step transition.
Protocol 1: Run Format (IGA)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Define Run Format (IGA)
Master Step Name = Define Run Format (IGA v2.1)
Step Type = No Outputs
Automations
Register Sample & Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Define Run Format - Assign Workflow and Flowcell Type to Samples & Set Next Steps to Remove from Workflow (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Define Run Format - Routing Script (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Step Data (Master Step Fields)
Protocol 2: NovaSeq Standard
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Make Bulk Pool for NovaSeq Standard
Master Step Name = Make Bulk Pool for NovaSeq Standard (IGA v2.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Automations
Register Sample & Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Pooling NovaSeq Standard - Show Warning Message (IGA v2.1)
Trigger Location = Pooling
Trigger Style = Automatic upon entry
Validate Inputs Flowcell Type and Number of Pools (IGA v2.1)
Trigger Location = Pooling
Trigger Style = Automatic upon exit
NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
Make Bulk Pool NovaSeq Standard - Calculate Volumes and Generate Hamilton Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Make Bulk Pool NovaSeq Standard - Validate Hamilton Output File Name if Present, Parse Instrument ID, Set Next Steps to Advance (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Validate Unique Indexes (IGA v2.1)
Trigger Location = Not Used
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Pooling
Label Uniqueness = On
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Well Sort Order = Column
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step 2: Dilute and Denature
Master Step Name = Dilute and Denature (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Validate Single Input (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Validate Library Tube Barcode (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
Dilute and Denature NovaSeq Standard - Generate Hamilton Library Tube Input File, Validate Run Setup, and Generate SampleSheet (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Dilute and Denature NovaSeq Standard - Set Next Steps to Remove from Workflow (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Dilute and Denature NovaSeq Standard - Routing Script (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Step Data (Master Step Fields)
Protocol 3: NovaSeq Xp
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Make Bulk Pool for NovaSeq Xp
Master Step Name = Make Bulk Pool for NovaSeq Xp (IGA v2.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Automations
Register Sample & Register Step Started (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Validate Inputs Flowcell Type and Single Pool (IGA v2.1)
Trigger Location = Pooling
Trigger Style = Automatic upon exit
NovaSeq Make Bulk Pool - Output Plate BPP Barcode Check (Duplicates Allowed) (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
Make Bulk Pool NovaSeq Xp - Reset Loading Workflow Type and Flowcell Type (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Make Bulk Pool NovaSeq Xp - Calculate Volumes and Generate Hamilton Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Set Flowcell Type and Next Step (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Validate Unique Indexes (IGA v2.1)
Trigger Location = Not Used
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Pooling
Label Uniqueness = On
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Well Sort Order = Row
Placement Pattern = Column
Record Details
Step Data (Master Step Fields)
Step 2: Dilute, Denature & ExAmp
Master Step Name = Dilute, Denature & ExAmp (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Variable
Automations
Dil/Den/ExAmp NovaSeq Xp - Generate Hamilton Consolidated Bulk Pool MakeBPP Input File and Validate Input Flowcell Type (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Dil/Den/ExAmp NovaSeq Xp - Validate Hamilton BPP Output File Name & Parse Instrument ID (IGA v2.1)
Dil/Den/ExAmp NovaSeq Xp - Calculate Volumes and Generate Incomplete WPP Driver File for Next Step (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Dil/Den/ExAmp NovaSeq Xp - Set Next Steps to Advance (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Set Flowcell Type and Next Step (IGA v2.1)
Trigger Location = Not Used
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Step Setup = Enabled
File Placeholders
Hamilton Consolidated MakeBPP Bulk Pool Input File
Description = This file contains consolidated Bulk Pool information to run the Hamilton MakeBPP method. It refers to previous Xp Make Bulk Pool steps in Clarity that all use the same BPP output plate name. Please run this file with the Hamilton MakeBPP method before continuing with this step.
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Load to Flowcell
Master Step Name = Load to Flowcell (IGA v2.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Validate Inputs and Selected Container (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon entry
Validate Flowcell Barcode with New Mask Fixes (IGA v2.1)
Trigger Location = Placement
Trigger Style = Automatic upon exit
Validate Run Setup and Generate Sample Sheet (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Load to Flowcell NovaSeq Xp - Generate Hamilton WPP Input File (IGA v2.1)
Trigger Location = Record Details
Trigger Style = Manual button
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Validate Flowcell Barcode (IGA v2.1)
Trigger Location = Not Used
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Protocol 4: AUTOMATED - NovaSeq Run
Protocol Type = Sequencing
Next Steps Configuration
Step 1: AUTOMATED - NovaSeq Run
Master Step Name = AUTOMATED - NovaSeq Run (IGA v2.1)
Step Type = Analysis
Measurement Generation = Variable
Automations
Register Step Completed (IGA v2.1)
Trigger Location = Step
Trigger Style = Automatic upon exit
Set Next Steps (IGA v2.1)
Trigger Location = Not Used
Show warning message and register step started at AUTOMATED step (IGA v2.1)
Trigger Location = Not Used
Queue
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Defaults =
User tasks for this page:
- Below, assign 'Loading Workflow Type', 'Flowcell Type', and the NovaSeq 'Final Loading Concentration (pM)'.
- Click 'Next Steps'.
Step File Placeholders
Log file - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Naming Convention = {PoolName}
Control Types
PhiX v3
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Well Sort Order = Column
Destination Containers
96 well plate
Default = 2
Decimal Places Displayed = 2
Liquid Handling Instrument ID
Text
Read Only
Apply Correction Factors
Text Dropdown
Required Field
Presets
None
IDPF
Quick reference checklist: Make Bulk Pool for NovaSeq Standard. i) pre Liquid Handler
Multiline Text
Read Only
Defaults =
User tasks for this page:
- Select 'Number Of Flowcells' and 'Min Per Sample Volume (ul)'
- 'Run' the Make Bulk Pool automation, and download resulting Hamilton Make Bulk Pool Input File
Quick reference checklist: Make Bulk Pool for NovaSeq Standard. ii) post Liquid Handler
Multiline Text
Read Only
Defaults =
User tasks for this page:
- After running MakeBPP on the liquid handler, upload resulting Hamilton Output File
- Click on 'Next Steps'
Step File Placeholders
Calculation Log - Automatically attached
Hamilton Make Bulk Pool Input File - Automatically attached
Hamilton file log - Automatically attached
Hamilton Output File - Manually uploaded
Custom Correction Factors - Manually uploaded
Index Correction Log - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Naming Convention = {InputItemName}
Reagent Kits
NaOH
Supplier = Illumina
Resuspension Buffer (RSB)
Supplier = Illumina
Tris-HCl
Supplier = Illumina
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Placement Pattern = Column
Destination Containers
Library Tube
Default = CTGTCTCTTATACACATCT
BaseSpace App Slug
Text Dropdown
Required Field
Custom Entries
Presets
Illumina-inc.bcl-convert.1.3.0
Illumina-inc.bcl-convert.1.2.0
BaseSpace Sequence Hub Analysis Workflow
Text
Required Field
Default = TSS Connect v1.1
BaseSpace Sequence Hub Configuration
Text Dropdown
Required Field
Presets
Run Monitoring And Storage
Run Monitoring Only
BaseSpace Sequence Hub Project Name
Text
Required Field
Custom Recipe Path
Text
Enable Secondary Analysis
Toggle Switch
Required Field
Default = Yes
Experiment Name
Text
Required Field
Index Read 1
Numeric Dropdown
Required Field
Custom Entries
Presets
10
6
Index Read 2
Numeric Dropdown
Required Field
Custom Entries
Presets
10
6
Liquid Handling Instrument ID
Text
Read Only
Output Folder
Text
Required Field
Paired End
Text Dropdown
Required Field
Presets
True
False
Quick reference checklist: Dilute and Denature.
Multiline Text
Read Only
Defaults =
User tasks for this page:
- Select NaOH/TrisHCl/RSB lots, and input run configuration
- 'Run' Dilute and Denature automation, download resulting input 'Hamilton Load to Library tube file'
- Click 'Next Steps' and then 'Finish Step' to move library tube through to 'AUTOMATED - NovaSeq Run'.
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
151
251
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
151
251
Required Yield Gbp
Numeric
Required Field
Default = 90
Run Mode
Text Dropdown
Read Only
Presets
S4
S1
SampleSheet Version
Text Dropdown
Required Field
Presets
V2
V1
Use Custom Index Read 1 Primer
Toggle Switch
Default = No
Use Custom Read 1 Primer
Toggle Switch
Required Field
Default = No
Use Custom Read 2 Primer
Toggle Switch
Required Field
Default = No
Use Custom Recipe
Toggle Switch
Required Field
Default = No
Workflow
Text
Read Only
Default = GenerateFASTQ
Workflow Type
Text Dropdown
Required Field
Presets
Dual Index
Single Index
Step File Placeholders
Sample Sheet - Automatically attached
Sample sheet Log File - Automatically attached
Hamilton Load to Library tube file - Automatically attached
Hamilton file log - Automatically attached
Biosample Manifest - Automatically attached
Sample Table (Table Columns - Global Fields)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Naming Convention = {PoolName}
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Well Sort Order = Row
Destination Containers
96 well plate
Default = 2
Decimal Places Displayed = 2
Apply Correction Factors
Text Dropdown
Required Field
Presets
None
IDPF
Quick reference checklist: Make Bulk Pool for NovaSeq Xp. i) pre Liquid Handler
Multiline Text
Read Only
Defaults =
User tasks for this page:
- Select 'Number Of Lanes' and 'Min Per Sample Volume (ul)'
- 'Run' the Make Bulk Pool automation
- Click 'Next Steps' and 'Finish Steps'. To add another Bulk Pool to this BPP, repeat Make Bulk Pool for NovaSeq Xp. Once your BPP contains the pools you need, continue on to Dilute and Denature to get the collated MakeBPP Liquid Handler input file.
Step File Placeholders
Log - Automatically attached
Hamilton Make Bulk Pool Input File - Automatically attached
Hamilton Input File Generation Log - Automatically attached
Description = Please upload the Hamilton output file from the MakeBPP run.
Attachment = Manual
Placement Pattern = Column
Destination Containers
96 well plate
Decimal Places Displayed = 0
DPX3 Volume (ul)
Numeric
Read Only
Decimal Places Displayed = 0
Liquid Handling Instrument ID
Text
Read Only
Quick reference checklist: Dilute, Denature and ExAmp
Multiline Text
Read Only
Defaults =
User tasks for this page:
- Input DPX/NaOH/RSB/TrisHCl lots
- Click 'Next Steps'
Step File Placeholders
Calculation File - Automatically attached
Log File - Automatically attached
Incomplete WPP Hamilton Files (DO NOT USE; REQUIRED FOR NEXT STEP!) - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Category
Naming Convention = {InputItemName}
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
Placement Pattern = Column
Destination Containers
SP
S1
S2
S4
Default = CTGTCTCTTATACACATCT
BaseSpace App Slug
Text Dropdown
Required Field
Custom Entries
Presets
Illumina-inc.bcl-convert.1.3.0
Illumina-inc.bcl-convert.1.2.0
BaseSpace Sequence Hub Analysis Workflow
Text
Required Field
Default = TSS Connect v1.1
BaseSpace Sequence Hub Configuration
Text Dropdown
Required Field
Presets
Run Monitoring And Storage
Run Monitoring Only
BaseSpace Sequence Hub Project Name
Text
Required Field
Custom Recipe Path
Text
Enable Secondary Analysis
Toggle Switch
Required Field
Default = Yes
Experiment Name
Text
Required Field
Index Read 1
Numeric Dropdown
Required Field
Custom Entries
Presets
10
6
Index Read 2
Numeric Dropdown
Required Field
Custom Entries
Presets
10
6
Library Tube Barcode
Text
Required Field
Output Folder
Text
Required Field
Paired End
Text Dropdown
Required Field
Presets
True
False
Quick reference checklist: Load To Flowcell.
Multiline Text
Read Only
Defaults =
User tasks for this page:
- Populate run configuration settings above
- 'Run' Load To Flowcell automation, download resulting 'Hamilton Input File (BPP to WPP to Flow Cell)' file
- 'Run' Validate Run Setup and Generate Sample Sheet (IGA v2.1) automation
- Click 'Next Steps' and then 'Finish Step' to move flowcell through to 'AUTOMATED - NovaSeq Run'
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
151
251
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
151
251
Required Yield Gbp
Numeric
Default = 90
SampleSheet Version
Text Dropdown
Required Field
Presets
V2
V1
Use Custom Index Read 1 Primer
Toggle Switch
Required Field
Default = No
Use Custom Read 1 Primer
Toggle Switch
Required Field
Default = No
Use Custom Read 2 Primer
Toggle Switch
Required Field
Default = No
Use Custom Recipe
Toggle Switch
Required Field
Default = No
Workflow
Text
Read Only
Default = GenerateFASTQ
Workflow Type
Text Dropdown
Required Field
Presets
Dual Index
Single Index
Step File Placeholders
Sample Sheet - Automatically attached
Log File - Automatically attached
Hamilton Input File (BPP to WPP to Flow Cell) - Automatically attached
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-[A-Z]{3}:: ) ) {fail ( ::Invalid Library Tube Barcode. This must be in the format CCxxxxxxx-CCC, where 'x' is a digit 0-9 and 'C' is an uppercase letter, e.g. LP1234567-ABC. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' -log {compoundOutputFileLuid1}"
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-q true \
-destLIMSID {compoundOutputFileLuid2} \
-t /opt/gls/clarity/extensions/IGA_2.1/hamilton_fast_prep/templatefiles/LoadToLibTubeFile_NovaSeqStd_template.csv \
-o Output_plate_name.csv \
-l {compoundOutputFileLuid3} && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-exp 'step.::Run Mode:: = input.::Flowcell Type:: ; if (!step.::Experiment Name::.matches(::[a-zA-Z0-9-_]+::)) { fail(::Experiment Name contains prohibited characters. Allowed characters are: a-z, A-Z, 0-9, -, and _::) }; if (step.::Workflow Type:: == ::No Index::) { if (step.::Index Read 1:: != 0) { fail(::Index Read 1 must be 0 if the Workflow Type is No Index.::) } } else { if (step.::Index Read 1:: == 0) { fail(::Index Read 1 must be greater than 0 if the Workflow Type is :: + step.::Workflow Type:: + ::.::) } }; if (step.::Paired End::.toBoolean() && step.::Read 2 Cycles:: == 0) { fail(::Read 2 Cycles must not be zero if it is Paired End read.::) }; if (step.::Workflow Type:: == ::Dual Index:: && step.::Index Read 2:: == 0) { fail(::Index Read 2 must not be zero if Workflow Type is Dual Index.::) }; if (step.::Workflow Type:: == ::No Index:: || step.::Workflow Type:: == ::Single Index::) { step.::Index Read 2:: = 0 }; if (!step.::Paired End::.toBoolean()) { step.::Read 2 Cycles:: = 0 }; if (input.::Flowcell Type::!=::SP:: && step.::Read 1 Cycles:: > 151) { fail(::Read 1 Cycles must not be larger than 151 if it is not SPrime Flowcell::) };if (input.::Flowcell Type::!=::SP:: && step.::Read 2 Cycles:: > 151) { fail(::Read 2 Cycles must not be larger than 151 if it is not SPrime Flowcell::) }; nextStep = ::REMOVE::' \
-log {compoundOutputFileLuid1} \
-t true \
&& if [[ '{udf:SampleSheet Version}' == 'V2' && '{udf:Enable Secondary Analysis}' == 'false' ]]; then \
templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_Std_V2.csv'; \
else \
templateFilename='/opt/gls/clarity/extensions/IGA_2.1/ss_converter_templates/NovaSeq_BCL2FASTQ_Samplesheet_Std_V1.csv'; \
fi \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {stepURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t $templateFilename \
-o {compoundOutputFileLuid0}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid0} \
-l {compoundOutputFileLuid1} \
&& if [[ '{udf:Enable Secondary Analysis}' == 'true' ]]; then \
PYTHONPATH=/opt/gls/clarity/extensions/IGA_2.1 python3 /opt/gls/clarity/extensions/IGA_2.1/ss_converter \
--input {compoundOutputFileLuid0}.csv \
--bssh-app {udf:BaseSpace App Slug} \
--stepURI {stepURI:v2} -u {username} -p {password} -q \
--destLIMSID {compoundOutputFileLuid0} 2>&1; \
fi && \
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
-i {stepURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/IGA_2.1/iga_novaseq/Biosample_Manifest.csv \
-o {compoundOutputFileLuid4}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid4} \
-l {compoundOutputFileLuid1}"
