CLE Lab: Pipeline scripts for Seq Runsheet and a Samplesheet for Feiyu

[tim-snyder-wustl]

• Add new workflow and protocol to WF chain
• File should be a TSV

Automate sample sheet for Feiyu so that he knows which samples of ours are in a sequencing run

• Need Runsheet for sequencer
• Sample sheet for Feiyu

It was decided this should be one file for simplicity.

[tim-snyder-wustl]

From Feiyu:

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Currently for different CLE assays, CLE lab will prepare a sample excel spreadsheet of each batch for me to launch the analysis workflow. My WDL workflow launcher script will parse this excel spreadsheet and then generate demux sample sheet for dragen demux task and sample information sheet for workflow inputs. The typical sample excel spreadsheet from CLE lab has below columns:

• Lane
• Flowcell ID
• Content_Desc
• Index
• Exceptions

A example sample spreadsheet for MyeloSeqHD assay is attached below.

MyeloSeq_070323_A00584_2870488.xlsx

[tim-snyder-wustl]

Runsheet will need these values from the furthest ancestor (CLE Specimen)

• patient name
• DOB
• sex

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• Lanes are comma-separated
• MRN - entity value
• MRN List - entity value
• Accession - Accesion Number, entity value should be brought in during ingest
• Assay

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Need to update CLE entities (that aren't Pools) to have / inherit:

• patient name
• DOB
• sex
• MRN