DReichLab / DReichLab/waldo

Add Coverage Field to Sample Site Updater Upload Template

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Dominant language
Python
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Description

I'd like to request adding a coverage field as an optional input column in the Sample Site Updater section of WALDO.

Motivation:
We would like to record coverage values reported in publications and supplementary materials at the time of sample annotation. Having coverage available as an uploadable field would enable future sanity checks comparing recorded coverage values against coverage calculated from our pulldown and downstream processing pipelines.

This would help identify potential metadata inconsistencies, sample mix-ups, transcription errors, or other discrepancies between published metadata and internally generated metrics.

Proposed Change
Add a new optional column: coverage
Allow coverage to be uploaded through the Sample Site Updater workflow alongside other sample metadata fields.
Store the value as sample-level metadata.

Use Case
When annotating a publication, we could enter the coverage reported by the authors. Later, we could compare those values against the calculated coverage generated on our end from pulldown data.

Benefits
Enables automated sanity checks between published and internally calculated coverage values.
Improves metadata validation and quality control.
Helps identify potential discrepancies early.
Reduces the need for external spreadsheets or manual tracking of coverage metadata.

Priority
Not urgently required for current workflows, but would be valuable infrastructure for future QC and metadata validation efforts.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Sample Site Updater upload workflow and inspect how existing optional sample metadata columns are accepted and stored. Add coverage alongside those fields, keeping it optional and sample-level. Done means uploads containing coverage succeed and the value is available for later metadata validation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
68/100

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