# 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](https://www.illumina.com) * Illumina COVIDSeqTest Box 4 * Supplier = Illumina * Catalog Number = 20043436 * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 = #### Automations
Calculate Total Samples * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Calculate AW1, AW2, AVL Reagent Volumes * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 | | | | % EtOH Prep Date | Date | | | | AW1 Concentrate (mL) | Numeric | | | | AW2 Concentrate (mL) | Numeric | | | | Buffer AVL (mL) | Numeric | | | | Carrier RNA-Buffer AVE (uL) | Numeric | | | | Elution Incubation End Time | Numeric | | | | Elution Incubation Start Time | Numeric | | | | EtOH for AW1 (mL) | Numeric | | | | EtOH for AW2 (mL) | Numeric | | | | Instruction Notes | Multiline Text | | | | No. of Preps | Numeric Dropdown | | | | Total Samples | 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 | | | ### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Calculate First Strand Synthesis Master Mix * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * Illumina COVIDSEQ Test Box 7 – 3072 Samples * Supplier = Illumina * Catalog Number = 20043439 * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Calculate COVIDSeq PCR 1 and PCR2 Master Mixes * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * Illumina COVIDSeqTest Box 3 – 3072 Samples * Supplier = Illumina * Catalog Number = 20043646 * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Calculate Tagmentation Master Mix * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * Illumina COVIDSeqTest Box 4 * Supplier = Illumina * Catalog Number = 20043436 * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Calculate PCR Master Mix * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Calculate ITB Volume * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Copy Concentration From QC Step * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step and Copy Concentration * Trigger Location = Not Used {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Copy Concentration * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Calculate Sample & RSB Volumes * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step and Copy Concentration * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Copy Concentration From QC Step * Trigger Location = Not Used {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Copy Concentration * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Calculate Molarity, Library Pool & RSB * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | 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

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | 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 {% code overflow="wrap" %} ```markup 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" ``` {% endcode %}
Validate Flowcell Barcode * Trigger Location = Placement * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Validate Run Setup and Generate Sample Sheet * Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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

| | 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 | | | | Custom Recipe Path | Text | | | | Experiment Name | Text | | | | Index Read 1 | Numeric Dropdown | | | | Index Read 2 | Numeric Dropdown | | | | Library Tube Barcode | Text | | | | Output Folder | Text | | | | Paired End | Text Dropdown | | | | Read 1 Cycles | Numeric Dropdown | | | | Read 2 Cycles | Numeric Dropdown | | | | Reverse Complement Workflow | Toggle Switch | | | | UMI - Read 1 Length | Numeric | | | | UMI - Read 1 Start From Cycle | Numeric | | | | UMI - Read 2 Length | Numeric | | | | UMI - Read 2 Start From Cycle | Numeric | | | | Use Custom Index Read 1 Primer | Toggle Switch | | | | Use Custom Read 1 Primer | Toggle Switch | | | | Use Custom Read 2 Primer | Toggle Switch | | | | Use Custom Recipe | Toggle Switch | | | | Workflow | Text | | | | Workflow Type | Text Dropdown | | | * 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

| | Derived Sample | Loading Workflow Type | Text Dropdown | Required Field |

Presets

| | 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 {% code overflow="wrap" %} ```markup 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" ``` {% endcode %}
Set Next Steps * Trigger Location = Not Used {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 {% code overflow="wrap" %} ```markup /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/parseCovidSeqRunReport.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid1} -g {compoundOutputFileLuid3} ``` {% endcode %}
#### 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 | | | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/clarity-lims/applications/viral-pathogen-protocols/covid-illumina-covidseq-v1.6.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.