Samples¶
The sample is the physical specimen from a subject. Samples own the sequencing files (VCF, BAM, FASTQ) and the metadata that describes how the sample was collected and processed.
Data model¶
| Field | Purpose |
|---|---|
id (UUID) |
Internal primary key |
display_id |
Human-readable identifier, unique per project |
subject_id |
Link to the subject this sample came from |
| Specimen metadata | Specimen type, collection date, etc. |
tags, properties |
Categorisation and flexible metadata |
Samples appear on orders via a many-to-many relationship. Each appearance
records a role (proband, mother, father, tumour, normal,
etc.) — so the same sample can be the proband in one order and the
mother in another.
Files¶
Sample files live under samples/{slug}/uploads/:
| File | Purpose |
|---|---|
*.vcf.gz (+ .tbi) |
Primary input to the variant browser. Must be bgzipped and tabix-indexed. |
*.bam (+ .bai) |
Aligned reads, useful for IGV inspection. |
*.fastq.gz |
Raw reads, when the pipeline does alignment. |
| Lab metadata | Any JSON / CSV supplied by the sequencing lab. |
See File Paths for the canonical layout.
VCF must be bgzipped and tabix-indexed
The VCF service requires .vcf.gz + .tbi to build the variant
browser cache. Uncompressed or non-indexed VCFs will not be parsed.
Sampleinfo and samplesheet¶
Two helpers generate lab-friendly derivatives of the sample record:
- Sampleinfo JSON — an aggregated view of the sample's metadata, useful as an input to pipelines that expect a structured manifest.
- Samplesheet CSV — an nf-core-compatible samplesheet derived from the
samples on an order, produced via
iflow orders samplesheet ORDER_ID. Useful for bulk pipeline submission.
UI¶
- Samples list —
/samples. - Sample detail —
/samples/{sample_id}. Shows metadata, the subject link, orders the sample participates in, and the file browser forsamples/{slug}/uploads/. - New sample —
/samples/new.
API¶
Base URL: https://miner.<env-domain>/api/v1/samples.
CLI¶
iflow samples list
iflow samples create --display-id S-2026-0042 --subject NA12878
iflow samples upload S-2026-0042 /path/to/S-2026-0042.vcf.gz