Illumina COVIDSeq v1.6

Overview

The Illumina COVIDSeq Workflow workflow includes the following functionality:

Preset Illumina COVIDSeq Workflow protocols that track samples through the quantitative detection of SARS-CoV-2 RNA from nasopharyngeal (NP), oropharyngeal (OP), and nasal swab as well as mid-turbinate specimens collected from individuals who meet COVID-19 clinical or epidemiological criteria.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Sample preparation for use on the NovaSeq 6000 Sequencing System.
Parsing of analysis results into Clarity LIMS.

Protocol 1: RNA Extraction (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Prep Sample (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Prep Sample (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeq Positive Control HT
  - Supplier = Illumina
  - Website = www.illumina.com
- Illumina COVIDSeqTest Box 4
  - Supplier = Illumina
  - Catalog Number = 20043436
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Instruction Notes
Multiline Text
Read Only
Default = For each sample, add 140 µl patient sample, dilution 3 CPC HT, or ELB HT (no template control) to a new 1.7 ml microcentrifuge tube.
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Purification of RNA - Spin (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Spin Purification of RNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- QIAmp Viral RNA Mini kit
  - Supplier = Qiagen
  - Catalog Number = (50) - 52904; (250) - 52906
  - Website = https://www.qiagen.com

Automations

Calculate Total Samples

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 \
-t false \
-h false \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0}"

Calculate AW1, AW2, AVL Reagent Volumes

Trigger Location = Record Details
Trigger Style = Manual button

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 -t false -h false \
-exp 'if (step.::No. of Preps:: == 50) {step.::AW1 Concentrate (mL):: = 19 ; step.::EtOH for AW1 (mL):: = 25 ; step.::AW2 Concentrate (mL):: = 13 ; step.::EtOH for AW2 (mL):: = 30} else {step.::AW1 Concentrate (mL):: = 98 ; step.::EtOH for AW1 (mL):: = 130 ; step.::AW2 Concentrate (mL):: = 66 ; step.::EtOH for AW2 (mL):: = 160} ; \
step.::Buffer AVL (mL):: = 0.56 * step.::Total Samples:: ; step.::Carrier RNA-Buffer AVE (uL):: = 10 * step.::Buffer AVL (mL):: ' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
% EtOH
Numeric
Default = 96
Range = 96 To 100
% EtOH Prep Date
Date
AW1 Concentrate (mL)
Numeric
AW2 Concentrate (mL)
Numeric
Buffer AVL (mL)
Numeric
Decimal Places Displayed = 0
Carrier RNA-Buffer AVE (uL)
Numeric
Decimal Places Displayed = 0
Elution Incubation End Time
Numeric
Elution Incubation Start Time
Numeric
EtOH for AW1 (mL)
Numeric
EtOH for AW2 (mL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Enter in No. of Preps before clicking on "Calculate AW1, AW2, AVL Reagent Volumes". Elute in 30 µl Buffer AVE instead of 60 µl. Incubate elution for at least 1 minute.
No. of Preps
Numeric Dropdown
Required Field
Custom Entries
Presets
250
50
Default = 250
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Anneal Sample (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Anneal Sample (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeq Test Box 5 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043648
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq Anneal Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 17 µl 65°C for 3 minutes Hold at 4°C
Instruction Notes
Multiline Text
Read Only
Default = Add 8.5 µl EPH3 HT to each well. Add 8.5 µl eluted sample to each well. Seal and shake at 1600 rpm for 1 minute. Centrifuge at 1000 × g for 1 minute.
Thermal Cycler Program Notes
Text
Default = COVIDSeq Anneal
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 2: cDNA Synthesis (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Synthesize First Strand cDNA (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Synthesize First Strand cDNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeq Test Box 6 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043647
  - Website = www.illumina.com

Automations

Calculate First Strand Synthesis Master Mix

Trigger Location = Record Details
Trigger Style = Manual button

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 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::FSA (uL):: = 9 * step.::Total Samples:: ; step.::RVT (uL):: = 1 * step.::Total Samples:: ' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq FSS Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 25 µl 25°C for 5 minutes 50°C for 10 minutes 80°C for 5 minutes Hold at 4°C
FSA (uL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Add 8 µl First Strand cDNA Master Mix to each well of the CDNA1 plate.
RVT (uL)
Numeric
Total Samples
Numeric
Required Field
Default = 0
Thermal Cycler Program
Text
Default = COVIDSeq FSS
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 3: Target Amplification (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Amplify cDNA (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Amplify cDNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeq Test Box 5 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043648
  - Website = www.illumina.com
- Illumina COVIDSEQ Test Box 7 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043439
  - Website = www.illumina.com

Automations

Calculate COVIDSeq PCR 1 and PCR2 Master Mixes

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::IPM HT for COVIDSeq PCR 1 Master Mix (uL):: = 15 * step.::Total Samples:: ; step.::CPP1 HT for COVIDSeq PCR 1 Master Mix (uL):: = 4.3 * step.::Total Samples:: ; step.::Nuclease-free water for COVIDSeq PCR 1 Master Mix (uL):: = 4.7 * step.::Total Samples:: ; step.::IPM HT for COVIDSeq PCR 2 Master Mix (uL):: = 15 * step.::Total Samples:: ; step.::CPP2 HT for COVIDSeq PCR 2 Master Mix (uL):: = 4.3 * step.::Total Samples:: ; step.::Nuclease-free water for COVIDSeq PCR 2 Master Mix (uL):: = 4.7 * step.::Total Samples::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq PCR Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 25 µl 98°C for 3 minutes 35 cycles of: 98°C for 15 seconds 65°C for 5 minutes Hold at 4°C
CPP1 HT for COVIDSeq PCR 1 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
CPP2 HT for COVIDSeq PCR 2 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
Instruction Notes
Multiline Text
Read Only
Default = Add 20 µl COVIDSeq PCR 1 Master Mix to each well of the COV1 plate corresponding to each well of the CDNA1 plate. Add 5 µl first strand cDNA synthesis from each well of the CDNA1 plate to the corresponding well of the COV1 plate. Add 20 µl COVIDSeq PCR 2 Master Mix to each well of the COV2 plate corresponding to each well of the CDNA1 plate. Add 5 µl first strand cDNA synthesis from each well of the CDNA1 plate to the corresponding well of the COV2 plate.
IPM HT for COVIDSeq PCR 1 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
IPM HT for COVIDSeq PCR 2 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
Nuclease-free water for COVIDSeq PCR 1 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
Nuclease-free water for COVIDSeq PCR 2 Master Mix (uL)
Numeric
Decimal Places Displayed = 0
Thermal Cycler Program
Text
Default = COVIDSeq PCR
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 4: Library Prep (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment PCR Amplicons (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Tagment PCR Amplicons (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSEQ Test Box 7 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043439
  - Website = www.illumina.com
- Illumina COVIDSeqTest Box 3 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043646
  - Website = www.illumina.com

Automations

Calculate Tagmentation Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::TB1 (uL):: = 12 * step.::Total Samples:: ; step.::eBLT (uL):: = 4 * step.::Total Samples:: ; step.::Nuclease-free water (uL):: = 20 * step.::Total Samples::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq TAG Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 50 µl 55°C for 5 minutes Hold at 10°C
eBLT (uL)
Numeric
Decimal Places Displayed = 0
Instruction Notes
Multiline Text
Read Only
Default = Add 30 µl Tagmentation Master Mix to each well in TAG1 plate.
Nuclease-free water (uL)
Numeric
Decimal Places Displayed = 0
TB1 (uL)
Numeric
Decimal Places Displayed = 0
Thermal Cycler Program
Text
Default = COVIDSeq TAG
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Post Tagmentation Clean Up (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Post Tagmentation Clean Up (Illumina COVIDSeq Workflow v1.6)
Step Type = No Outputs
Reagent Kits
- Illumina COVIDSeq Test Box 2 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043434
  - Website = www.illumina.com
- Illumina COVIDSeqTest Box 4
  - Supplier = Illumina
  - Catalog Number = 20043436
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Amplify Tagmented Amplicons (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Amplify Tagmented Amplicons (Illumina COVIDSeq Workflow v1.6)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Reagent Kits
- Illumina COVIDSeq Test Box 5 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043648
  - Website = www.illumina.com

Automations

Calculate PCR Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::EPM HT (uL):: = 24 * step.::Total Samples:: ; step.::Nuclease-free water (uL):: = 24 * step.::Total Samples::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Add Labels

Label Groups
- IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000
- Illumina DNA-RNA UD Indexes Set A B C D Tagmentation
- Illumina DNA-RNA UD Indexes Set A Tagmentation
- Illumina DNA-RNA UD Indexes Set B Tagmentation
- Illumina DNA-RNA UD Indexes Set C Tagmentation
- Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq TAG PCR Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option and set to 100°C Set the reaction volume to 50 µl 72°C for 3 minutes 98°C for 3 minutes 7 cycles of: 98°C for 20 seconds 60°C for 30 seconds 72°C for 1 minute 72°C for 3 minutes Hold at 10°C
EPM HT (uL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Add 40 µl PCR Master Mix to each well.
Nuclease-free water (uL)
Numeric
Thermal Cycler Program
Text
Default = COVIDSeq TAG PCR
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 4: Pool and Clean Up Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Pool and Clean Up Libraries (Illumina COVIDSeq Workflow v1.6)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Illumina COVIDSeqTest Box 3 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043646
  - Website = www.illumina.com

Automations

Calculate ITB Volume

Trigger Location = Record Details
Trigger Style = Manual button

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 'step.::ITB (uL):: = 0.9 * (55 * step.::Total Pooled ITB Tubes::) ' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column

Placement = Enabled

Defaults
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- 1x8 Strip Tube
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
80% EtOH Date
Date
Instruction Notes
Multiline Text
Read Only
Default = Enter in Total Pooled ITB Tubes to Calculate ITB (uL) volume. Transfer 50 µl supernatant from each Pooled ITB tube to a new microcentrifuge tube.
ITB (uL)
Numeric
Total Pooled ITB Tubes
Numeric
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 5: Quantification (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Quantify Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Quantify Libraries - Qubit (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Assign QC flags (Qubit QC)

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"

Copy Concentration From QC Step

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 -t false -h false -exp 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Set Next Step and Copy Concentration

Trigger Location = Not Used

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 -t false -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Criteria 1 - Operator
Text
Default = >=
Criteria 1 - Source Data Field
Text
Default = Concentration
Criteria 1 - Threshold Value
Numeric
Default = 2
Criteria 2 - Operator
Text
Default = <>=
Criteria 2 - Source Data Field
Text
Default = Concentration
Criteria 2 - Threshold Value
Numeric
Default = 30
Step File Placeholders
- Log - Automatically attached
- QC Log File - Automatically attached
- QC Result File - Manually uploaded
- Upload File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  Sample Name
  Built-in
  Measurement
  Concentration
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Conc. Units
  Text
  Project
  Project Name
  Built-in

Step 2: Dilute Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeqTest Box 3 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043646
  - Website = www.illumina.com

Automations

Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 \
 -t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-log {compoundOutputFileLuid0}"

Calculate Sample & RSB Volumes

Trigger Location = Record Details
Trigger Style = Manual button

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 'output.::SampleVolume (uL):: = 0.1 * step.::Final Volume (uL):: ; output.::RSB (uL):: = step.::Final Volume (uL):: - output.::SampleVolume (uL):: ' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Dilution Factor
Text
Read Only
Default = 1:10
Final Volume (uL)
Numeric
Instruction Notes
Multiline Text
Default = Enter Final Volume (uL) then click on "Calculate Sample & RSB Volumes" for dilution volumes.
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  RSB (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  SampleVolume (uL)
  Numeric
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

Step 3: Quantify Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Quantify Libraries - Qubit (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Assign QC flags (Qubit QC)

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"

Set Next Step and Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 -t false -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Copy Concentration From QC Step

Trigger Location = Not Used

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 -t false -h false -exp 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Criteria 1 - Operator
Text
Default = >=
Criteria 1 - Source Data Field
Text
Default = Concentration
Criteria 1 - Threshold Value
Numeric
Default = 2
Criteria 2 - Operator
Text
Default = <>=
Criteria 2 - Source Data Field
Text
Default = Concentration
Criteria 2 - Threshold Value
Numeric
Default = 30
Step File Placeholders
- Log - Automatically attached
- QC Log File - Automatically attached
- QC Result File - Manually uploaded
- Upload File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  Sample Name
  Built-in
  Measurement
  Concentration
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Conc. Units
  Text
  Project
  Project Name
  Built-in

Step 4: Normalize Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Normalize Libraries (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeqTest Box 3 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043646
  - Website = www.illumina.com

Automations

Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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 \
 -t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-log {compoundOutputFileLuid0}"

Calculate Molarity, Library Pool & RSB

Trigger Location = Record Details
Trigger Style = Manual button

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 'output.::Starting Molarity (nM):: = (output.::Concentration:: / (660 * 400)) * 1000000 ; output.::Library Pool (uL):: = step.::Final Molarity (nM):: * step.::Final Volume (uL):: / output.::Starting Molarity (nM):: ; output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Library Pool (uL):: ' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Final Molarity (nM)
Numeric
Default = 4
Final Volume (uL)
Numeric
Default = 30
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  RSB (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Starting Molarity (nM)
  Numeric
  Default = 0
  Derived Sample
  Library Pool (uL)
  Numeric
  Default = 0
  Project
  Project Name
  Built-in

Step 5: Pool and Dilute Libraries (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Pool and Dilute Libraries (Illumina COVIDSeq Workflow v1.6)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Illumina COVIDSeqTest Box 3 – 3072 Samples
  - Supplier = Illumina
  - Catalog Number = 20043646
  - Website = www.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Instruction Notes
Multiline Text
Read Only
Default = For each set of 384 samples, combine 25 µl of each normalized pool containing index adapter set A, B, C, D in a new microcentrifuge tube. Do not combine pools with the same index adapter set. This step produces a final pool of 384 samples for one flow cell lane. For each flow cell lane, dilute each 384 sample pool with RSB HT as follows. These steps produce 30 µl 0.5 nM pooled library. Combine 3.75 µl library from the 384-sample pool with 26.25 µl RSB. Vortex, and then centrifuge briefly. The resulting final loading concentration is 100 pM.
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 6: NovaSeq 6000 Xp Setup (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: NovaSeq Denature & ExAmp (Illumina COVIDSeq Workflow v1.6)

Master Step Name = NovaSeq Denature & ExAmp (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}_WP{OutputItemNumber}
Reagent Kits
- DPX1
  - Supplier = Illumina
  - Catalog Number = 20019916
- DPX2
  - Supplier = Illumina
  - Catalog Number = 20019917
- DPX3
  - Supplier = Illumina
  - Catalog Number = 20019918
- NaOH
- Tris-HCl

Automations

Calculate DPX1, DPX2, DPX3

Trigger Location = Record Details
Trigger Style = Manual button

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 'step.::DPX1 Volume (ul):: = 315 * step.::No. of Lanes:: ; step.::DPX2 Volume (ul):: = 45 * step.::No. of Lanes:: ; step.::DPX3 Volume (ul):: = 165 * step.::No. of Lanes:: ; output.::Flowcell Type:: = step.::Flowcell Type::; output.::Loading Workflow Type:: = step.::Loading Workflow Type::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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 \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Flowcell Type
  Text Dropdown
  Required Field
  Presets
  SP
  S1
  S2
  S4
  Derived Sample
  Loading Workflow Type
  Text Dropdown
  Required Field
  Presets
  NovaSeq Standard
  NovaSeq Xp
  [Remove from workflow]
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
0.2 N NaOH per pool (uL)
Numeric
Read Only
Default = 7
0.2 N NaOH Prep Date
Date
400 mM Tris-HCl per pool (uL)
Numeric
Read Only
Default = 8
400 mM Tris-HCl Prep Date
Date
DPX1 Volume (ul)
Numeric
Read Only
Decimal Places Displayed = 0
DPX2 Volume (ul)
Numeric
Read Only
Decimal Places Displayed = 0
DPX3 Volume (ul)
Numeric
Read Only
Decimal Places Displayed = 0
Flowcell Type
Text
Read Only
Default = S4
Instruction Notes
Multiline Text
Read Only
Default = Enter the No. of Lanes for your S4 flow cell to calculate DPX 1, DPX2 and DPX 3 volumes.
Loading Workflow Type
Text
Read Only
Default = NovaSeq Xp
No. of Lanes
Numeric
Required Field
Default = 4
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Flowcell Type
  Text Dropdown
  Required Field
  Presets
  SP
  S1
  S2
  S4
  Derived Sample
  Loading Workflow Type
  Text Dropdown
  Required Field
  Presets
  NovaSeq Standard
  NovaSeq Xp
  [Remove from workflow]
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Load to Flowcell (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Load to Flowcell (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Validate Inputs and Selected Container

Trigger Location = Step
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_flowcell_for_input_pools -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -validateSelectedContainer true"

Validate Flowcell Barcode

Trigger Location = Placement
Trigger Style = Automatic upon exit

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 (input.::Flowcell Type:: == ::SP:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S1:: && !output.container.name.matches( ::[A-Z0-9]{5}DR[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S2:: && !output.container.name.matches( ::[A-Z0-9]{5}DM[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; if (input.::Flowcell Type:: == ::S4:: && !output.container.name.matches( ::[A-Z0-9]{5}DS[A-Z0-9]{2}:: ) ) {fail ( ::Invalid Flowcell Barcode. Please verify and try again.:: ) } ; output.::Flowcell Type:: = input.::Flowcell Type:: ; output.::Loading Workflow Type:: = input.::Loading Workflow Type::' \
        -log {compoundOutputFileLuid1}"

Validate Run Setup and Generate Sample Sheet

Trigger Location = Record Details
Trigger Style = Manual button

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 '{udf:Validation Script}' \
        -log {compoundOutputFileLuid1} \
        -t true \
&& if [ '{udf:Reverse Complement Workflow}' == 'true' ]; then \
  templateFilename='NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv'; \
elif [ '{udf:Reverse Complement Workflow}' == 'false' ]; then \
  templateFilename='NovaSeq_BCL2FASTQ_Samplesheet.csv'; \
else echo 'UDF Reverse Complement Workflow is empty or undefined.'; exit -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/conf/driverfiletemplates/$templateFilename \
        -o {compoundOutputFileLuid0}.csv \
        -q true \
        -destLIMSID {compoundOutputFileLuid0} \
        -l {compoundOutputFileLuid1}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Flowcell Type
  Text Dropdown
  Required Field
  Presets
  SP
  S1
  S2
  S4
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers
- S4

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
BaseSpace Sequence Hub Configuration
Text Dropdown
Required Field
Presets
Not Used
Run Monitoring Only
Run Monitoring And Storage
Custom Recipe Path
Text
Experiment Name
Text
Required Field
Index Read 1
Numeric Dropdown
Required Field
Custom Entries
Presets
0
6
8
Range = 0 To 20
Decimal Places Displayed = 0
Index Read 2
Numeric Dropdown
Required Field
Custom Entries
Presets
0
6
8
Range = 0 To 20
Decimal Places Displayed = 0
Library Tube Barcode
Text
Required Field
Output Folder
Text
Required Field
Paired End
Text Dropdown
Required Field
Presets
True
False
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
251
151
101
51
Range = 1 To 251
Decimal Places Displayed = 0
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Presets
251
151
101
51
Range = 0 To 251
Decimal Places Displayed = 0
Reverse Complement Workflow
Toggle Switch
Required Field
Default = Yes
UMI - Read 1 Length
Numeric
Range From 1
UMI - Read 1 Start From Cycle
Numeric
Range From 1
UMI - Read 2 Length
Numeric
Range From 1
UMI - Read 2 Start From Cycle
Numeric
Range From 1
Use Custom Index Read 1 Primer
Toggle Switch
Default = None Set
Use Custom Read 1 Primer
Toggle Switch
Default = None Set
Use Custom Read 2 Primer
Toggle Switch
Default = None Set
Use Custom Recipe
Toggle Switch
Required Field
Default = No
Workflow
Text
Required Field
Default = GenerateFASTQ
Workflow Type
Text Dropdown
Required Field
Presets
No Index
Single Index
Dual Index
Custom
Step File Placeholders
- Sample Sheet - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Flowcell Type
  Text Dropdown
  Required Field
  Presets
  SP
  S1
  S2
  S4
  Derived Sample
  Loading Workflow Type
  Text Dropdown
  Required Field
  Presets
  NovaSeq Standard
  NovaSeq Xp
  [Remove from workflow]
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 7: AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)

Master Step Name = AUTOMATED - NovaSeq Run (Illumina COVIDSeq Workflow v1.6)
Step Type = Analysis
Measurement Generation = Variable
Naming Convention = Lane {InputWellLocation}
Reagent Kits
- Buffer Cartridge
  - Supplier = Illumina
- Cluster Cartridge
  - Supplier = Illumina
- SBS Cartridge
  - Supplier = Illumina

Automations

Update Lane Number

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "sleep 10 && /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 (input.::Loading Workflow Type:: == ::NovaSeq Standard::) { output.::name:: = ::Lane :: + step.::Lane Counter::; output.::name:: = output.::name::.split(::\\.::)[0] + :::1::; step.::Lane Counter::++; }' \
        -log {compoundOutputFileLuid3} \
        -t true \
&& /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.::Lane Counter:: = 1' \
        -log {compoundOutputFileLuid3} \
        -t true"

Set Next Steps

Trigger Location = Not Used

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 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Current Cycle
Numeric
Read Only
Decimal Places Displayed = 0
Current Read
Numeric
Read Only
Decimal Places Displayed = 0
Firmware Version
Text
Read Only
Flow Cell Expiration Date
Date
Read Only
Flow Cell ID
Text
Read Only
Flow Cell Lot Number
Text
Read Only
Flow Cell Mode
Text
Read Only
Flow Cell Part Number
Text
Read Only
Flow Cell Side
Text
Read Only
Instrument Control Software Version
Text
Read Only
Instrument ID
Text
Read Only
Instrument Type
Text
Read Only
Loading Workflow Type
Text
Read Only
Output Folder
Text
Read Only
RTA Version
Text
Read Only
Run ID
Text
Read Only
Run Status
Text
Read Only
Sequencing Log
Multiline Text
Read Only
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  % Aligned R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Aligned R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Bases >=Q30 R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Bases >=Q30 R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Error Rate R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Error Rate R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  % Phasing R1
  Numeric
  Read Only
  Decimal Places Displayed = 3
  Container
  % Phasing R2
  Numeric
  Read Only
  Decimal Places Displayed = 3
  Container
  % Prephasing R1
  Numeric
  Read Only
  Decimal Places Displayed = 3
  Container
  % Prephasing R2
  Numeric
  Read Only
  Decimal Places Displayed = 3
  Container
  %PF R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  %PF R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  Container Name
  Built-in
  Container
  Cluster Density (K/mm^2) R1
  Numeric
  Read Only
  Container
  Cluster Density (K/mm^2) R2
  Numeric
  Read Only
  Container
  Intensity Cycle 1 R1
  Numeric
  Read Only
  Container
  Intensity Cycle 1 R2
  Numeric
  Read Only
  Container
  LIMS ID (Container)
  Built-in
  Container
  Reads PF (M) R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  Reads PF (M) R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  Well
  Built-in
  Container
  Yield PF (Gb) R1
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Container
  Yield PF (Gb) R2
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 8: Analysis Results (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Data Analysis

Next Steps Configuration

Step 1: Analysis Results (Illumina COVIDSeq Workflow v1.6)

Master Step Name = COVIDSeq Analysis Results (Illumina COVIDSeq Workflow v1.6)
Step Type = Demultiplexing
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} (FASTQ reads) {AppliedReagentLabels}

Automations

CovidSEQ: Parse TSV Run Report

Trigger Location = Record Details
Trigger Style = Manual button

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/parseCovidSeqRunReport.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid1} -g {compoundOutputFileLuid3}

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
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
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Record Details

Step Data
- Step Data Heading = WARNING: It might take several minutes to parse the TSV Run Report
Step File Placeholders
- Log - Automatically attached
- COVIDSeq TSV_Run Report File - Manually uploaded
- COVIDSeq_RunReport PDF - Manually uploaded
- Parsing Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Measurement
  Consensus Sequence
  Text
  Read Only
  Measurement
  Control Type
  Text
  Read Only
  Measurement
  Human Control
  Text
  Read Only
  Measurement
  Index ID
  Text
  Read Only
  Measurement
  Index ID for Control Sample
  Text
  Read Only
  Measurement
  Index Set
  Text
  Read Only
  Measurement
  Index Set for Control Sample
  Text
  Read Only
  Measurement
  Internal Control
  Text
  Read Only
  Measurement
  Lane
  Numeric
  Read Only
  Measurement
  Lane for Control Sample
  Numeric
  Read Only
  Measurement
  Quality Control
  Text
  Read Only
  Measurement
  Result
  Text
  Read Only
  Measurement
  SARS-CoV-2
  Text
  Read Only
  Measurement
  SARS-CoV-2 for Control Sample
  Text
  Read Only
  Project
  Project Name
  Built-in

PreviousReal-Time RT-PCR Prep v1.1 NextRespiratory Virus Panel v1.0

Last updated 8 months ago

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