Seq Lab: Flowcell Scheduling Smartsheets App

[billtell]

Provide a way for the Seq Lab to schedule work and load Flowcells.

[billtell]

• [ ] Ingest needs to write to Billing, Master Tracking Sheet (Date Ingested, Index, Library Type, Targeted Reads), Builder Sheet
• [ ] Builder Sheet

  qPCR node writes to update new relationships (dilution and pooling) and molarity information group into new Pools and assign to tech be able to distinguish flowcell pools - send to flowcell builder sheet

• [ ] Sheet automation to move samples down the line
• [ ] Make it so that techs can claim work
• [ ] Look into conditional formatting to show differences (Dilutions, Pools, etc.)
• [ ] Flowcell / Flowcell Lane Builder Sheet

  Sum up total reads in a lane Check index compatability may have to reference Billing Info sheet

• [ ] Final Flowcell Sheet

[billtell]

Builder Sheet Column Behavior

• Next Step = drop down, manual
• Pool ESP ID = write from qpcr node
• SR# = cell reference
• Drop Date = cell reference
• Project = cell reference
• Library Type = cell reference / join in delimited string of child rows
• Requested Reads (M) = cell reference / sum children
• Requested Bases (Gb) = cell reference / sum children
• ESP Entity = cell reference / write from qpcr node
• ESP Barcode = cell reference / write from qpcr node
• Pool Amount (uL) = manual entry(?) / sum children
• Pool Group = write from qpcr node
• Pool Relatives Checked into Freezer = manual
• Expected Molarity (nM/uL) = Client Assessed Molarity ? / cell reference?
• qPCR Molarity (nM) = write from qpcr node
• Average Library Size (bp) = write from qpcr node
• qPCR Volume (µl) - write from qpcr node
• qPCR Date = write from qpcr node
• qPCR Tech = dropdown / manual entry
• Results Validation Tech = dropdown / manual entry
• Plate barcode
• Dilution (nM) = write from qpcr node
• Total Dilution Volume (µl)
• Sample Volume for Dilution (µL)
• Buffer Volume for Dilution (uL)
• Dilution Tech = dropdown / manual entry
• Dilution Group = manual entry
• Customer Sample Name = cell reference
• Index Name = cell reference
• i7 Index = cell reference
• i5 Index = cell reference
• i7 Index trimmed = cell reference
• i5 Index trimmer = cell reference
• Library Count = count / sum children
• Notes / Comments = manual entry

[billtell]

1. Written from qPCR Node

These variables are automatically populated from the qPCR node.

•   Pool ESP ID
•   ESP Entity
•   ESP Barcode
•   Pool Group
•   qPCR Molarity (nM)
•   Average Library Size (bp)
•   qPCR Volume (µl)
•   qPCR Date
•   Dilution (nM)

2. Derived from Cell References

These variables pull their values directly from specific cell references in your data source.

•   SR#
•   Drop Date
•   Project
•   Customer Sample Name
•   Index Name
•   i7 Index
•   i5 Index
•   i7 Index trimmed
•   i5 Index trimmed
•   Expected Molarity (nM/uL) (possibly from cell reference)
•   Library Type (partially, also joins child rows)
•   ESP Entity (partially, also written from qPCR node)
•   ESP Barcode (partially, also written from qPCR node)

3. Summed from Child Rows

These variables aggregate data from child rows, typically by summing numerical values.

•   Requested Reads (M)
•   Requested Bases (Gb)
•   Pool Amount (uL) (also involves manual entry)
•   Library Count

4. Manual Entry

These variables require manual input from users.

•   Pool Amount (uL) (also involves summing children)
•   Pool Relatives Checked into Freezer
•   Notes / Comments
•   Dilution Group

5. Dropdown / Manual Entry

These variables can be selected from a dropdown menu or entered manually if the desired option isn’t available.

•   Next Step
•   qPCR Tech
•   Results Validation Tech
•   Dilution Tech

6. Combination Methods

These variables use multiple methods to determine their values, such as combining cell references with other operations.

•   Library Type: Cell reference and joins delimited strings of child rows
•   Requested Reads (M): Cell reference and sums children
•   Requested Bases (Gb): Cell reference and sums children
•   ESP Entity: Cell reference and written from qPCR node
•   ESP Barcode: Cell reference and written from qPCR node
•   Pool Amount (uL): Manual entry and sums children
•   Expected Molarity (nM/uL): Client assessed molarity and/or cell reference

7. Additional Variables Without Specific Descriptions

For variables that weren’t fully described, assumptions are made based on naming conventions.

•   Plate Barcode: Likely a unique identifier, possibly manually entered or auto-generated.
•   Total Dilution Volume (µl): Possibly calculated from other dilution variables.
•   Sample Volume for Dilution (µL): Likely derived from experimental setup or manual input.
•   Buffer Volume for Dilution (uL): Similar to sample volume, possibly calculated or manually entered.

[billtell]

• [ ] invokables.js function
• create sample results dictionary
• send to endpoint
• [ ] add as onchange on Complete column - complete column is not specified in yaml, might have to be a UI

[billtell]

• [ ] invokables.py function

[billtell]

• [ ] SmartsheetsBuilder class

[billtell]

• prod_sample_import_from_samplesheet.py

Testing infrustructure

[billtell]

• Added Average Concentration (ng/µl)
• Removed Dilution (nM), only going to use Molarity (nM) for all sample types

[billtell]

Smartsheet Builder Update Scenarios

• [ ] Existing Entity - Update Info

• [ ] New Library - New Library Row

• [ ] New Library Dilution - Add Library Dilution Row as parent of library

• [ ] New Pool - Look up hierarchy and child entity esp info

• [ ] New Pool Dilution of an existing Pool - add pool parent row

• Determine entity type = Library / Library Dilution / Pool / Pool Dilution

• Determine New / Existing

[billtell]

"{\"result\": {\"code\": 1123, \"errorCode\": 1123, \"message\": \"Specifying multiple row locations is not yet supported. Each row must use the same row location attribute and value (toBottom, toTop, parentId, siblingId, above)\", \"name\": \"ApiError\", \"recommendation\": \"Do not retry without fixing the problem. \", \"refId\": \"8183f94f-24b0-446a-a2bb-524f7bd34af1\", \"shouldRetry\": false, \"statusCode\": 400}}"

[LMT337]

Initial Library/Pool row writes to Builder/Billing sheets updates: #486