API Endpoint Reference

Interactive Documentation

Each service ships its own OpenAPI schema at /openapi.json and Swagger / ReDoc UIs at /docs and /redoc. Browse the live schema for your environment — the paths below use the production domain; staging uses *.stg.iflow.intelliseq.com.

• Admin Service — Swagger | ReDoc
• Compute Service — Swagger | ReDoc
• Files Service — Swagger | ReDoc
• Miner Service — Swagger | ReDoc
• Report Service — Swagger | ReDoc
• VCF Service — Swagger | ReDoc
• Audit Service — Swagger | ReDoc

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Admin Service

Base URL: https://admin.iflow.intelliseq.com/api/v1

Organizations

Method	Endpoint	Description
GET	/orgs	List organizations

Projects

Method	Endpoint	Description
GET	/projects	List all projects
GET	/projects/{id}	Get project details
GET	/projects/{id}/credentials	Get project credentials (for file service)

Users

Method	Endpoint	Description
GET	/users/me/default-context	Get user's default project
PUT	/users/me/default-context	Set user's default project

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Compute Service

Base URL: https://compute.iflow.intelliseq.com/api/v1

Pipelines

Method	Endpoint	Description
GET	/pipelines	List all pipelines
POST	/pipelines	Create new pipeline
GET	/pipelines/{id}	Get pipeline by ID
GET	/pipelines/slug/{slug}	Get pipeline by slug (latest version)
GET	/pipelines/slug/{slug}?version=1.0.0	Get specific version
GET	/pipelines/slug/{slug}/versions	List all versions

Runs

Method	Endpoint	Description
GET	/runs	List runs for project
POST	/runs	Submit new run
GET	/runs/{id}	Get run details
GET	/runs/{id}/outputs	Get run output files
DELETE	/runs/{id}	Cancel run
GET	/runs/by-order/{order_id}	List runs for an order

---

Miner Service

Base URL: https://miner.iflow.intelliseq.com/api/v1

Subjects

Method	Endpoint	Description
GET	/subjects	List subjects
POST	/subjects	Create subject
GET	/subjects/{id}	Get subject details
PATCH	/subjects/{id}	Update subject
DELETE	/subjects/{id}	Delete subject (cascades to samples)

Samples

Method	Endpoint	Description
GET	/samples	List samples
POST	/samples	Create sample
GET	/samples/{id}	Get sample details
PATCH	/samples/{id}	Update sample
DELETE	/samples/{id}	Delete sample
GET	/samples/{id}/sampleinfo	Generate pipeline-ready JSON

Orders

Method	Endpoint	Description
GET	/orders	List orders (filter by status, priority, assignee)
POST	/orders	Create order
GET	/orders/{id}	Get order details
PUT	/orders/{id}	Update order
DELETE	/orders/{id}	Delete order (only for non-signed orders)
POST	/orders/{id}/transition	Transition order status (body {"to": "<status>"})
GET	/orders/{id}/samplesheet	Generate nf-core samplesheet CSV
GET	/orders/{id}/samples	List samples in order
POST	/orders/{id}/samples/{sample_id}	Add sample to order (body {"role": "proband"})
DELETE	/orders/{id}/samples/{sample_id}	Remove sample from order
GET	/orders/{id}/labflow	Get current labflow state (stage, assignee, available transitions)

Labflows

Method	Endpoint	Description
GET	/labflows	List labflow definitions visible to the project
GET	/labflows/{id}	Get labflow definition including stages and transitions

Variants (read-only)

Method	Endpoint	Description
GET	/variants	List variants in the catalogue (filter by region, gene)
GET	/variants/{id}	Variant detail
GET	/samples/{id}/variants	Sample-level variants

---

Files Service

Base URL: https://files.iflow.intelliseq.com/api/v1

Files

Method	Endpoint	Description
GET	/files?project_id=ID&path=/	List files in path
GET	/files/download-url?project_id=ID&path=file.txt	Get signed download URL
POST	/files/upload-url?project_id=ID	Get signed upload URL
POST	/files/copy?project_id=ID	Copy file within bucket
POST	/files/move?project_id=ID	Move/rename file within bucket
DELETE	/files?project_id=ID&path=file.txt	Delete file

File Download (Two-Step)

Downloading a file is a two-step process: first get a signed URL, then download from it.

# Step 1: Get signed download URL (valid 15 minutes)
curl -s "https://files.iflow.intelliseq.com/api/v1/files/download-url?project_id=$PROJECT_ID&path=client-resources/report_template.docx" \
  -H "Authorization: Bearer $TOKEN" | jq .

# Response:
# {"url": "https://storage.googleapis.com/bucket/...", "expires_in_seconds": 900}

# Step 2: Download file from signed URL (no auth needed)
SIGNED_URL=$(curl -s "https://files.iflow.intelliseq.com/api/v1/files/download-url?project_id=$PROJECT_ID&path=client-resources/report_template.docx" \
  -H "Authorization: Bearer $TOKEN" | jq -r .url)
curl -o report_template.docx "$SIGNED_URL"

File Upload (Two-Step)

Uploading is also two-step: get a signed URL, then PUT the file.

# Step 1: Get signed upload URL
curl -s -X POST "https://files.iflow.intelliseq.com/api/v1/files/upload-url?project_id=$PROJECT_ID" \
  -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"path": "samples/S1/uploads/sample.vcf.gz", "content_type": "application/gzip"}' | jq .

# Response:
# {"url": "https://storage.googleapis.com/bucket/...", "expires_in_seconds": 900}

# Step 2: Upload file to signed URL (no auth needed)
curl -X PUT "$SIGNED_URL" \
  -H "Content-Type: application/gzip" \
  --data-binary @sample.vcf.gz

List Files

curl -s "https://files.iflow.intelliseq.com/api/v1/files?project_id=$PROJECT_ID&path=client-resources/" \
  -H "Authorization: Bearer $TOKEN" | jq .

---

Report Service

Base URL: https://report.iflow.intelliseq.com/api/v1

Reports

Method	Endpoint	Description
GET	/reports	List reports (filter by order_id, status, template_type)
POST	/reports	Create a report for an order
GET	/reports/{id}	Get report detail
PATCH	/reports/{id}	Update draft report (summary, notes, template_type)
DELETE	/reports/{id}	Delete a draft report (not allowed once signed)

Variant associations

Method	Endpoint	Description
GET	/reports/{id}/variants	List variants on the report
POST	/reports/{id}/variants	Add a variant with optional overrides
PATCH	/reports/{id}/variants/{variant_id}	Update per-report overrides
DELETE	/reports/{id}/variants/{variant_id}	Remove variant from report

Comments and snapshots

Method	Endpoint	Description
GET	/reports/{id}/comments	List comments (filter by type)
POST	/reports/{id}/comments	Post a comment (body {"comment": "...", "type": "review"})
PATCH	/reports/{id}/comments/{comment_id}	Edit or resolve
GET	/reports/{id}/snapshots	List snapshots
POST	/reports/{id}/snapshots	Create a snapshot

Sign-off (UI-driven)

The sign-off confirmation flow is HTMX-driven and lives at /{report_id}/signoff/* — see Sign-off PDF for the endpoint list. These endpoints are not intended for direct API consumers; the atomic Approve-and-Sign must run through the web UI.

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VCF Service

Base URL: https://vcf.iflow.intelliseq.com/api/v1

Method	Endpoint	Description
GET	/orders/{order_id}/variants	Paginated variant list for an order
GET	/orders/{order_id}/variants/{variant_id}	Single variant detail
GET	/orders/{order_id}/status	Build / ingestion status for the order's VCF cache

---

Audit Service

Base URL: https://audit.iflow.intelliseq.com/api/v1

Method	Endpoint	Description
GET	/events	Query audit events (filter by entity, action, date range)
GET	/events/{id}	Audit event detail

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Common Headers

All API requests require:

Authorization: Bearer <access_token>
Content-Type: application/json

Project-scoped endpoints (miner, compute, files) also require:

X-Project-ID: <project_uuid>

X-Project-ID is the UUID of your project, obtained from GET /api/v1/projects on admin-service. Admin-service endpoints do not require this header. See Authentication for details.

Error Responses

Status	Description
400	Bad request - invalid parameters
401	Unauthorized - missing or invalid token
403	Forbidden - insufficient permissions
404	Not found - resource doesn't exist
409	Conflict - resource already exists
500	Server error

Example error response:

{
  "detail": "Pipeline 'hereditary-mock' version '1.0.0' already exists. Use force=True to overwrite."
}