Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Select First Workflow Step (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Step Data (Master Step Fields)
Step File Placeholders
Master Step Name = Batch DNA Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = Standards
Derived Sample Generation = Fixed, 1
Instrument Types
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement Pattern = Same Shape
Destination Containers
Step Data (Master Step Fields)
Step File Placeholders
Master Step Name: Make WGA (ILASS Infinium Genotyping Assay v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Instrument Types
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement Pattern = Same Shape
Destination Containers
Step Data (Master Step Fields)
Master Step Name = Make WGA (ILASS Infinium Genotyping Assay v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Instrument Types
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement Pattern = Same Shape
Destination Containers
Step Data (Master Step Fields)
Master Step Name = Amplify WGA Manual (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Step Data (Master Step Fields)
Master Step Name = Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Instrument Types
Tecan EVO
Step Data (Master Step Fields)
Master Step Name = Precipitate DNA Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Instrument Types
Tecan EVO
Step Data (Master Step Fields)
Master Step Name = Resuspend DNA Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Instrument Types
Tecan EVO
Step Data (Master Step Fields)
Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Instrument Types
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement Pattern = Row
Destination Containers
Step Data (Master Step Fields)
Master Step Name = Prepare Hyb Chamber Manual (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Reagent Kits
PB2-Infinium
Step Data (Master Step Fields)
Master Step Name = Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Reagent Kits
PB1-Infinium
Step Data (Master Step Fields)
Master Step Name = Extend and Stain BeadChips Automated (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Instrument Types
Tecan EVO
Step Data (Master Step Fields)
Master Step Name = Wash and Coat BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Reagent Kits
PB1-Infinium
Step Data (Master Step Fields)
Protocol Type = Other
Next Steps Configuration
Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Instrument Types
iScan
Step Data (Master Step Fields)
Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.0)
Step Type = No Outputs
Step Data (Master Step Fields)
Log - Automatically attached
AssayRunLog - Manually uploaded
Hamilton Star
Vendor = Hamilton
96 well plate
Plate Manifest - Manually uploaded
Log - Automatically attached
Plate Transfer Plan - Manually uploaded
AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
Plating Source Barcode
Text
Hamilton Star
Vendor = Hamilton
Reagent Kits
AAX-Infinium
Supplier = Illumina
MA1-Infinium
Supplier = Illumina
MA2-Infinium
Supplier = Illumina
96 well plate
Plate Transfer Plan
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
Container
Field Name
Field Type
Options
Additional Options and Dropdown Items
Related Source Container
Text
Hamilton Star
Vendor = Hamilton
Reagent Kits
AAX-Infinium
Supplier = Illumina
MA1-Infinium
Supplier = Illumina
MA2-Infinium
Supplier = Illumina
96 well plate
Plate Transfer Plan
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Instruction Notes
Multiline Text
Read Only
Default = Incubate the WGA plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
Source DNA Plate Barcode
Text
Vendor = Tecan
Reagent Kits
FMS-Infinium
Supplier = Illumina
Instruction Notes
Multiline Text
Read Only
Plate Transfer Plan
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Vendor = Tecan
Reagent Kits
PMX-Infinium
Supplier = Illumina
Comment
Multiline Text
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
IsRecombined
Toggle Switch
Vendor = Tecan
Reagent Kits
IBX-Infinium
Supplier = Illumina
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Tecan EVO
Vendor = Tecan
Infinium Genotyping Array EX-24
Infinium Genotyping Array EX-48
Plate Transfer Plan
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Supplier = Illumina
Instruction Notes
Multiline Text
Read Only
Default = Add 400 µl PB2 to the top and bottom wells of each beadchip subchamber in the hybridization chamber.
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Supplier = Illumina
Instruction Notes
Multiline Text
Read Only
Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Vendor = Tecan
Reagent Kits
ATX-Infinium
Supplier = Illumina
EML-Infinium
Supplier = Illumina
LX1-Infinium
Supplier = Illumina
LX2-Infinium
Supplier = Illumina
PB1-Infinium
Supplier = Illumina
STX-Infinium
Supplier = Illumina
XC3-Infinium
Supplier = Illumina
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
IsRecombined
Toggle Switch
Supplier = Illumina
XC4-Infinium
Supplier = Illumina
Instruction Notes
Multiline Text
Read Only
Default = Add 310 ml PB1 to the PB1 wash dish. Add 310 ml XC4 to the XC4 wash dish.
Step File Placeholders
Log - Automatically attached
AssayRunLog - Manually uploaded
Vendor = Illumina
Instrument
Text
Read Only
Instrument Run ID
Text
Read Only
Run Start Time
Text
Read Only
Run Complete Time
Text
Read Only
Run Status
Text
Read Only
Failure Reason
Text
Read Only
Log
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
BeadChip Name
Text
Read Only
Analysis Start Time
Text
Read Only
Analysis Complete Time
Text
Read Only
Analysis Status
Text
Read Only
Log
Multiline Text
Read Only
Step File Placeholders
Log - Automatically attached
Sample Table (Global Step Fields)
Derived Sample
Field Name
Field Type
Options
Additional Options and Dropdown Items
BeadChip Name
Text
Read Only
Field Name
Field Type
Options
Additional Options and Dropdown Items
First Workflow Step Options
Text Dropdown
Required Field
Presets
Run Make WGA Step Manually
Run Batch DNA Step on Hamilton
Run Make WGA Step on Hamilton
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
100% 2-Propanol Prep Date
Date
Batch ID
Text
Read Only
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Batch ID
Text
Read Only
Comment
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
BeadChip Barcode
Text
Read Only
Instrument Type
Text
Read Only
Field Name
Field Type
Options
Additional Options and Dropdown Items
Analysis Configuration ID
Text
Required Field
Analysis Run Name
Text
Required Field
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:validateSampleCount -min 1 -max 1"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}"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}"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}"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}"bash -c -l "/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( step.::Analysis Run Name::.length()>255 ){ fail( ::Analysis Run Name exceeds maximum length of 255:: )}; if( !step.::Analysis Run Name::.matches(::^(?![wW][fF][rR]\\..*)(^[0-9a-zA-Z-_\\.]*$)::)) { fail( ::Analysis Run Name must consist of only alphanumeric, underscore, hyphen and period characters and cannot start with wfr.:: ) }; ' \
-log {compoundOutputFileLuid0} \
-t true \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/iscan-automation.jar \
script:start_process_analysis -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}"Plating Source Well
Text
Related WGA Container
Text
Default = No
Source DNA Plate Barcode
Text
Default = No
Source DNA Plate Barcode
Text
Sample Section
Text
Read Only
Imaging Result
Text
Sample Section
Text
Read Only
Analysis Result
Text
Read Only
