AmpliSeq for Illumina Myeloid Panel
Overview
The AmpliSeq for Illumina Myeloid Panel includes the following functionality:
| • | Preconfigured AmpliSeq for Illumina Myeloid Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA or total RNA using the AmpliSeq for Illumina workflow. |
| • | 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. |
| • | There is no extraction protocol in this workflow because the samples are already extracted. |
Protocol 1: DNA Library Prep (AmpliSeq for Illumina Myeloid Panel v1.0)
Step 1: Dilute RNA (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 1: Dilute RNA (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = RNA with concentration
Output = Diluted RNA (10-200 ng)
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Desired Concentration (ng/uL) |
| • | Numeric |
| – | Range 20 - 50 |
| – | Multiline Text Fields |
| – | Directions |
| – | Default = If enough RNA is available, dilute to intermediate concentration ~20-50 ng/uL. |
| – | Read only |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample |
| – | Single-line text |
| – | Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
| – | Nuclease-free water (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Sample Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Total Volume (uL) |
| – | Derived Sample |
| – | Numeric |
Automation - Script description
| • | Copy Concentration and Set Sample Volume |
| • | 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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]
| • | Calculate Input Amount |
| • | Trigger location: Record Details |
| – | Trigger Style: 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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]
| • | Copy Desired 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 'output.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]
[Optional] Next Steps:
| • | Qubit (AmpliSeq for Illumina Myeloid Panel v1.0) |
| • | Reverse Transcribe RNA (AmpliSeq for Illumina Myeloid Panel v1.0) |
Start Next Step - manual
Assign Next Step - Manual
Safe stopping point.
Step 2: Qubit (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 2: Qubit (AmpliSeq for Illumina v1.0)
Step Type: Standard QC
Input = Diluted RNA (2-200 ng)
Output = Measurement
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Criteria 1 - Source Data FieldText |
| – | Default = Concentration |
| • | Criteria 1 - Operator |
| – | Text |
| – | Default = >= |
| – | Criteria 1 - Threshold Value |
| – | Numeric |
| – | Criteria 2 - Source Data Field |
| – | Text |
| – | Default = Concentration |
| – | Criteria 2 - Operator |
| – | Text |
| – | Default = <= |
| – | Criteria 2 - Threshold Value |
| – | Numeric |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| – | QC Log File |
| – | Auto |
| – | QC Result File |
| – | Auto |
| – | Upload File |
| – | Manual |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample and Measurement |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample and Measurment |
| – | Text |
Automation - Script description
| • | Assign QC Flags |
| • | 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}"
Start Next Step - Manual
Assign Next Step - Automatic
Safe stopping point.
Step 3: Dilute RNA to Final Concentration (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 3: Dilute RNA (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = Diluted RNA with concentration
Output = Diluted RNA (10-200 ng)
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Desired Concentration (ng/uL) |
| • | Numeric |
| – | Range 20 - 50 |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample |
| – | Numeric |
| – | Copied from previous step |
| – | Conc. Units |
| – | Derived Sample |
| – | Single-line text |
| – | Copied from previous step |
| – | Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
| – | Calculated |
| – | Nuclease-free water (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Calculated |
| – | Sample Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Calculated |
| – | Total Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Calculated |
Automation - Script description
| • | Copy Concentration and Set Sample Volume |
| • | 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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]
| • | Calculate Input Amount |
| • | 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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]
| • | Set Next Step - Advance and Set Desired Conc |
| • | 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:: ; output.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]
Start Next Step - Automatic
Assign Next Step - Automatic
Must move forward.
Step 4: Reverse Transcribe (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 4: Reverse Transcribe RNA (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = RNA with concentration
Output = Reverse Transcribed RNA
Reagent Kits =
| • | AmpliSeq cDNA Synthesis for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 20022654 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
| – | Column |
Record Details
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Default = RT |
| – | 5X AmpliSeq cDNA Reaction Mix (uL) |
| – | Numeric |
| – | 10X AmpliSeq RT Enzyme Mix (uL) |
| – | Numeric |
| – | Nuclease-free water (uL) |
| – | Numeric |
| – | Prep Input Volume (uL) |
| – | Numeric |
| – | Calculated |
| – | Prep Input Amount (ng) |
| – | Numeric |
| – | User input |
| – | Mandatory |
| – | Range - 10-100 << remains as 1-100ng from standard |
| – | Total Samples |
| – | Numeric |
| – | Calculated |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample |
| – | Text |
| – | Total Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
Automation - Script description
| • | Copy Concentration, Total Volume and Input Amount - Myeloid |
| – | 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 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /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.::Desired Concentration (ng/uL):: ; \output.::Conc. Units:: = input.::Conc. Units:: ; \output.::Total Volume (uL):: = input.::Total Volume (uL):: ; \output.::Input Amount (ng):: = input.::Input Amount (ng):: ; \step.::Desired Concentration (ng/uL):: = input.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]
| • | Calculate Prep Input - Myeloid Panel |
| • | 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 true \
-h false \
-exp 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 3.5) {step.::Nuclease-free water (uL):: = (3.5 - step.::Prep Input Volume (uL)::) * step.::Total Samples::} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5' \
-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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe stopping point
Step 5: Amplify cDNA Targets (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 5: Amplify cDNA Targets Standard (AmpliSeq for Illumina v1.0) >> New Master Step with with no reps = variable output = 1.
Step Type: Standard
Input = Reverse Transcribed RNA
Output = cDNA
Reagent Kits =
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
| • | AmpliSeq Myeloid Panel for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 20024478 |
| – | Website - www.illumina.com |
Place Samples = 96 well plate
| • | Placement - Manual |
| • | Users should manually place the RNA pool 1 samples in Columns 7, 9, 11 and the pool 2 samples in 8, 10, 12 |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
| – | Auto placement |
Record Details
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Default = AMP_RNA |
| – | 5X AmpliSeq HiFi Mix (uL) |
| – | Numeric |
| – | Decimal Places = 2 |
| – | Nuclease-free water (uL) |
| – | Numeric |
| – | Decimal Places = 2 |
| – | PCR Cycles |
| – | Numeric |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table ColumnsABLE COLUMNS |
| • | None |
Automation - Script description
| • | Set Sample Type and Calculate Master Mix - Myeloid Panel |
| • | 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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /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.::Sample Type:: = ::cDNA:: ; \
step.::5X AmpliSeq HiFi Mix (uL):: = 4.0 * step.::Total Samples:: * 1.1 ; \
step.::Nuclease-free water (uL):: = 7.0 * step.::Total Samples:: * 1.1' \
-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}["]
| • | Routing Samples - Myeloid Panel |
| – | Trigger location: Step |
| – | 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.0' \
--STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Myeloid Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' ["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point.
Protocol 2: DNA Library Prep (AmpliSeq for Illumina Myeloid Panel v1.0)
Step 1: Dilute DNA (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 1: Dilute DNA (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = DNA with concentration
Output = Diluted DNA (20-200 ng)
Reagent Kits =
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Desired Concentration (ng/uL) |
| • | Numeric |
| – | Range 20 - 50 |
| – | Multiline text fields |
| – | Directions |
| – | Default = If enough DNA is available, dilute to intermediate concentration ~20-50 ng/uL. |
| – | Read only |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample |
| – | Single-line text |
| – | Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
| – | Low TE (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Sample Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Total Volume (uL) |
| – | Derived Sample |
| – | Numeric |
Automation - Script description
| • | Copy Concentration and Set Sample Volume |
| • | 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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]
| • | Calculate Input Amount |
| • | 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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]
[Optional] Next Steps:
| • | Qubit (AmpliSeq for Illumina Meyloid Panel v1.0) |
| • | Amplify Targets (AmpliSeq for Illumina Myeloid Panel v1.0) |
Start Next Step - Manual
Assign Next Step - Manual
Safe Stopping Point
Step 2: Qubit (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 2: Qubit (AmpliSeq for Illumina v1.0)
Step Type: Standard QC
Input = Diluted DNA (20-200 ng)
Output = Measurement
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Criteria 1 - Source Data Field |
| • | Text |
| – | Default = Concentration |
| • | Criteria 1 - Operator |
| – | Text |
| – | Default = >= |
| – | Criteria 1 - Threshold Value |
| – | Numeric |
| – | Criteria 2 - Source Data Field |
| – | Text |
| – | Default = Concentration |
| – | Criteria 2 - Operator |
| – | Text |
| – | Default = <= |
| – | Criteria 2 - Threshold Value |
| – | Numeric |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| – | QC Log File |
| – | Auto |
| – | QC Result File |
| – | Auto |
| – | Upload File |
| – | Manual |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample and measurement |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample and measurement |
| – | Text |
Automation - Script description
| • | Assign QC Flags |
| • | 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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point
Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 3: Dilute DNA (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = DNA with concentration
Output = Diluted DNA (2-200 ng)
Reagent Kits =
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | Tube |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Desired Concentration (ng/uL) |
| • | Numeric |
| – | Range 20 - 50 |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | Concentration |
| • | Derived Sample |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample |
| – | Single-line text |
| – | Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
| – | Low TE (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Sample Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Total Volume (uL) |
| – | Derived Sample |
| – | Numeric |
Automation - Script description
| • | Copy Concentration and Set Sample Volume |
| • | 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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]
| • | Calculate Input Amount |
| • | 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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (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}["]
Start Next Step - Automatic
Assign Next Step - Automatic
Must move forward.
Step 4: Amplify DNA Targets (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 4: Amplify Targets Duplicates (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = Diluted DNA (20-200 ng)
Output = Amplified DNA Variable Output = 2
Sample Name = {InputItemName}_{OutputItemSubsetNumber}
Reagent Kits =
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
| • | AmpliSeq Myeloid Panel for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 20024478 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
| – | Users should manually place the DNA pool 1 samples in Columns 1-3 and the pool 2 samples in 4-6 |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Default = AMP |
| – | PCR Cycles |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
| • | Table Columns |
| • | 5X AmpliSeq HiFi Mix (uL) |
| • | Derived Sample |
| – | Numeric |
| – | Concentration |
| – | Derived Sample |
| – | Numeric |
| – | Conc. Units |
| – | Derived Sample |
| – | Text |
| • | Nuclease-free water (uL) |
| • | Derived Sample |
| – | Numeric |
| – | Calculated |
| – | Prep Input Volume (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Calculated |
| – | Prep Input Amount (ng) |
| – | Derived Sample |
| – | Numeric |
| – | User input |
| – | Mandatory |
| – | Range - 2-200 |
Automation - Script description
Copy Concentration, Total Volume and Input Amount
| • | 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:: ; output.::Total Volume (uL):: = input.::Total Volume (uL):: ; output.::Input Amount (ng):: = input.::Input Amount (ng):: ; output.::5X AmpliSeq HiFi Mix (uL):: = 4.5'\-log {compoundOutputFileLuid0}["]
| • | Calculate Prep Input - Myeloid |
| • | 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 'output.::Prep Input Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Concentration:: ; \if (output.::Prep Input Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 13.5 - output.::Prep Input Volume (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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point
Step 5: Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 5: Transfer RNA and DNA Amplicons (AmpliSeq for Illumina v1.0)
Step Type: Pooling
Input = cDNA and DNA amplicon samples
Output = Pooled cDNA and DNA samples
Pooling
| • | Turn off Label Uniqueness - since the samples are not indexed yet and we need to pool them |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
| • | Proof of concept on API page for automatic plating (does not exist yet) |
| – | Samples are pooled together with their pair then placed in the appropriate well on the 96 well plate |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Step File Placeholder |
| • | Log |
| • | Auto |
| • | Table Columns |
Automation - Script description
| • | 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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point
Step 6: Partially Digested Amplicons (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 6: Partially Digested Amplicons (AmpliSeq for Illumina v1.0)
Step Type: No Outputs
Input = Pooled samples
Output = Partially Digested Amplicons
Reagent Kits =
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Default = FUPA |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | 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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point.
Step 7: Ligate Indexes (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 7: Ligate Indexes (AmpliSeq for Illumina v1.0)
Step Type: Add Labels
Input = Partially Digested Amplicons
Output = Ligated Libraries
Reagent Kits =
| • | AmpliSeq Library PLUS for IlluminaSupplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
Add Labels - Index List (5.x)
| • | AmpliSeq CD Indexes Set A for Illumina - AmpliSeq CD Indexes Set A for Illumina-label-sheet.xlsx |
| • | AmpliSeq CD Indexes Set B for Illumina - AmpliSeq CD Indexes Set B for Illumina-label-sheet.xlsx |
| • | AmpliSeq CD Indexes Set C for Illumina - AmpliSeq CD Indexes Set C for Illumina-label-sheet.xlsx |
| • | AmpliSeq CD Indexes Set D for Illumina - AmpliSeq CD Indexes Set D for Illumina-label-sheet.xlsx |
| • | AmpliSeq UD Indexes for Illumina (24 Indexes) - AmpliSeq UD Indexes for Illumina (24 Indexes)-label-sheet.xlsx |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Default = LIGATE |
| • | Step File Placeholders |
| • | Log File |
| • | Auto |
| • | Table Columns |
| • | AmpliSeq Workflow |
| • | Derived Sample |
| – | Text Dropdown |
| – | Drop-down Items: |
| – | Standard Workflow |
| – | Equalizer Workflow |
| – | Mandatory |
Automation - Script description
| • | 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 ::' \ ???? REMOVE ???? -log {compoundOutputFileLuid0}["]
Route AmpliSeq Samples - Myeloid Panel
| • | Trigger location: Step |
| – | 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \--FIELD_NAME 'AmpliSeq Workflow' \--FIELD_VALUE 'Standard Workflow' \--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.0' \--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME 'AmpliSeq Workflow' \--FIELD_VALUE 'Equalizer Workflow' \--WORKFLOW 'Equalizer AmpliSeq for Illumina Myeloid Panel v1.0' \--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS'["]
Start Next Step - Manual, Automatic
Assign Next Step - Manual, Automatic
Safe Stopping Point
Protocol 3: Standard Workflow (AmpliSeq for Illumina Childhood Cancer Panel v1.0)
Step 1: Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 1: Clean Up Library (AmpliSeq for Illumina v1.0)
Step Type: No Output
Input = Ligated Libraries
Output = Cleaned Up Libraries
Reagent Kits =
| • | Agencourt AMPure XP Beads |
| • | Supplier - Thermo |
| – | Cat. # - NC9959336; NC9933872 |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | 70% EtOH Prep Date Date |
| • | Step File Placeholders |
| • | Log File |
| • | Auto |
Automation - Script description
| • | 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}["]
Start Next Step - Automatic
Assign Next Step - Automatic
Must move forward
Step 2: Amplify Library (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 2: Amplify Library (AmpliSeq for Illumina v1.0)
Step Type: No Output
Input = Cleaned Up Libraries
Output = Amplified Libraries
Reagent Kits =
| • | Agencourt AMPure XP BeadsSupplier - Thermo |
| – | Cat. # - NC9959336; NC9933872 |
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Derived Sample |
| – | Text |
| – | Total Samples |
| – | Derived Sample |
| – | Numeric |
| – | Default = 0 |
| – | 1X Lib AMP Mix (uL) |
| – | Derived Sample |
| – | Numeric |
| – | 10X Library Amp Primers (uL) |
| – | Derived Sample |
| – | Numeric |
| – | Groups of Defaults Standard Workflow default = AMP_7 |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | Calculate Total Samples and Calculate 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} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /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 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \-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}["]
Start Next Step - Manual
Assign Next Step - Automatic
Safe Stopping Point
Step 3: Perform Second Clean Up (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 3: Perform Second Clean Up (AmpliSeq for Illumina BRCA Panel v1.0)
Step Type: Standard
Input = Amplified Libraries
Output = Cleaned Up Amplified Libraries
Reagent Kits =
| • | Agencourt AMPure XP Beads |
| • | Supplier - Thermo |
| – | Cat. # - NC9959336; NC9933872 |
| • | AmpliSeq Library PLUS for Illumina |
| • | Supplier - Illumina |
| – | Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103 |
| – | Website - www.illumina.com |
Placement
| • | Master Step |
| • | None |
| • | Step |
| • | 96 well plate |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | 70% EtOH Prep Date Date |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | 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}["]
Start Next Step - Manual, Automatic
Assign Next Step - Manual, Automatic
Safe Stopping Point, Must move forward.
Protocol 4: Equalizer Workflow (AmpliSeq for Illumina Childhood Cancer Panel v1.0)
Step 1: Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 1: Clean Up Library (AmpliSeq for Illumina v1.0)
Step Type: No Output
Input = Ligated Libraries
Output = Cleaned Up Libraries
Reagent Kits =
| • | Agencourt AMPure XP Beads |
| • | Supplier - Thermo |
| – | Cat. # - NC9959336; NC9933872 |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | 70% EtOH Prep Date |
| • | Date |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | 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}["]
Start Next Step - Manual, Automatic
Assign Next Step - Manual, Automatic
Safe Stopping Point, Must move forward.
Step 2: Amplify Library (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 2: Amplify Library (AmpliSeq for Illumina v1.0)
Step Type: No Output
Input = Cleaned Up Libraries
Output = Amplified Libraries
Reagent Kits =
| • | Agencourt AMPure XP Beads |
| • | AmpliSeq Library PLUS for Illumina |
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Total Samples |
| – | Numeric |
| – | Default = 0 |
| – | 1X Lib AMP Mix (uL) |
| – | Numeric |
| – | 10X Library Amp Primers (uL) |
| – | Numeric |
| – | Group of Defaults = Equalizer Workflow |
| – | Thermal Cycler Program = Equal |
| • | Step File Placeholder |
| • | Log |
| • | Auto |
Automation - Script description
| • | Calculate Total Samples and Calculate 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} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /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 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \-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}["]
Start Next Step - Manual, Automatic
Assign Next Step - Manual, Automatic
Safe Stopping Point, Must move forward.
Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = Amplified Libraries
Output = Cleaned Up Libraries
Reagent Kits =
| • | AmpliSeq Library Equalizer for Illumina |
| • | Supplier = Illumina |
| – | Cat. # = |
| – | Website = www.illumina.com |
Place Samples = 96 well plate
Record Details =
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | 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}["]
Automatic Transition
Start Next Step - Automatic
Assign Next Step - Automatic
Safe Stopping Point, Must move forward.
Step 4: Elute Library (AmpliSeq for Illumina Myeloid Panel v1.0)
Master Step 4: Elute Library (AmpliSeq for Illumina v1.0)
Step Type: Standard
Input = Cleaned Up Libraries
Output = Final Library
Reagent Kits =
| • | AmpliSeq Library Equalizer for Illumina |
| • | Supplier = Illumina |
| – | Cat. # = |
| – | Website = www.illumina.com |
Place Samples = 96 well plate
Record Details =
| • | Step Data |
| • | Master Step Fields |
| • | Thermal Cycler Program |
| • | Text |
| – | Present ELUTE |
| • | Step File Placeholders |
| • | Log |
| • | Auto |
Automation - Script description
| • | 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}["]
Start Next Step - Manual, Automatic
Assign Next Step - Manual, Automatic
Safe Stopping Point, Must move forward.
