Assigning Files to Samples

After file discovery, sequencing files need to be linked to the correct samples. SeqDesk provides both automatic matching and manual assignment.

Auto-Detect Matching

The matching engine compares discovered file identifiers against sample records:

1. Extract the sample identifier from the filename
2. Compare against sampleId, sampleAlias, and sampleTitle (in priority order)
3. Calculate a confidence score (0–1)
4. Suggest the match to the facility admin

Confidence Levels

High-confidence matches occur when the filename identifier exactly matches the sample alias or ID. Medium-confidence matches may result from partial name overlaps.

Manual Assignment

For files that do not auto-match or need correction:

1. Navigate to the Files page or the order’s file tab
2. Browse the discovered files list
3. For each file pair (R1/R2), select the target sample from a dropdown
4. Confirm the assignment

The file browser shows:

• File path relative to the data base path
• File size
• Current assignment status (assigned / unassigned)
• The sample it is assigned to (if any)

What Gets Stored

When files are assigned, a Read record is created linking the files to the sample:

File paths are stored relative to the data base path and resolved at runtime.

Bulk Assignment

For orders with many samples, the auto-detect feature can process all samples at once:

1. Open the order detail page
2. Click Discover Files
3. The system scans and suggests matches for all samples
4. Review the suggestions
5. Confirm to apply all high-confidence matches

Low-confidence matches are left unassigned for manual review.

Requirements for Pipelines

Before a pipeline can run on a study:

• All included samples must have at least one read record
• Read files must exist at the configured paths
• For paired-end pipelines, both R1 and R2 must be assigned

The pipeline launcher validates these requirements before allowing a run to start. See Running a Pipeline.