Quick Reference¶

All iflow CLI commands at a glance. For detailed guides, see the linked pages.

Quick Start¶

# Option A: Interactive setup wizard (recommended for first time)
iflow configure

# Option B: Manual setup
iflow login --token YOUR_PAT_TOKEN
iflow config select-project
iflow pipelines list
iflow analyses submit --pipeline wdl-minimal --watch

Setup Wizard¶

Command	Description
`iflow configure`	Interactive setup (env, login, project)

iflow configure    # Guided first-time setup

Authentication¶

Command	Description
`iflow login`	Authenticate (use `--token` for PAT)
`iflow logout`	Clear credentials
`iflow status`	Check auth status

iflow login                          # Opens browser (Device Flow)
iflow login --token YOUR_PAT_TOKEN   # PAT auth (headless/CI)

Configuration¶

Command	Description
`iflow config show`	Show current config and project
`iflow config env [ENV]`	Get/set environment (prod, stg, dev)
`iflow config select-project`	Interactive project selection
`iflow config clear-project`	Clear project selection
`iflow config set KEY VALUE`	Set config value
`iflow config reset`	Reset to defaults

iflow config select-project        # Interactive
iflow config select-project ID     # Direct
iflow config env prod              # Switch to production

File Operations¶

Guide: File Operations

Command	Description
`iflow files ls [PATH]`	List files
`iflow files download PATH`	Download file
`iflow files upload LOCAL REMOTE`	Upload file
`iflow files mv SOURCE DEST`	Move/rename file
`iflow files rm PATH`	Delete file

Option	Description
`-p, --project`	Project ID (uses default)
`-o, --output`	Output path (download)
`-y, --yes`	Skip confirmation (mv, rm)
`--curl`	Output curl command

iflow files ls data/
iflow files download outputs/report.pdf -o report.pdf
iflow files upload sample.vcf data/sample.vcf
iflow files mv data/old.vcf data/new.vcf
iflow files rm data/old-output.vcf --yes

Pipelines¶

Guide: Pipeline Workflows

Command	Description
`iflow pipelines list`	List available pipelines
`iflow pipelines info SLUG`	Get pipeline details
`iflow pipelines versions SLUG`	List all versions
`iflow pipelines describe SLUG`	Show inputs/outputs
`iflow pipelines add --url URL`	Add new pipeline

Option	Description
`-V, --version`	Specific version
`-f, --force`	Overwrite existing (add)
`--curl`	Output curl command

iflow pipelines list
iflow pipelines info hereditary-mock
iflow pipelines versions hereditary-mock
iflow pipelines describe hereditary-mock -V 1.0.0
iflow pipelines add --url https://workflows.example.com/.../workflow.wdl

Analyses¶

Guide: Managing Analyses

Command	Description
`iflow analyses submit --pipeline SLUG`	Submit analysis
`iflow analyses list`	List analyses
`iflow analyses last`	Get most recent analysis
`iflow analyses status ID`	Get analysis details
`iflow analyses watch ID`	Watch until complete
`iflow analyses outputs ID`	List semantic outputs
`iflow analyses cancel ID`	Cancel analysis

Option	Description
`-p, --project`	Project ID (uses default)
`--pipeline`	Pipeline slug (required for submit)
`-V, --pipeline-version`	Pipeline version
`-o, --order-id`	Associate with order
`--sample-id`	Sample display ID to link (resolved to UUID)
`--sample-uuid`	Sample UUID to link (bypasses resolution)
`-P, --param`	Parameter KEY=VALUE (repeatable)
`-t, --tag`	Tag (repeatable)
`--callback-url`	Webhook URL
`--watch`	Watch after submit
`--curl`	Output curl command

iflow analyses submit --pipeline wdl-minimal --watch
iflow analyses submit --pipeline hereditary-mock -V 1.0.0 \
  -P case_id=case-001 \
  -P child_fastq=data/R1.fastq.gz \
  --watch
iflow analyses list --order-id ORDER_ID
iflow analyses status RUN_ID

Subjects¶

Guide: Managing Subjects

Command	Description
`iflow subjects list`	List subjects
`iflow subjects create --display-id ID`	Create subject
`iflow subjects get ID`	Get subject details
`iflow subjects update ID`	Update subject fields
`iflow subjects delete ID`	Delete subject (cascades to samples)

Option	Description
`-p, --project`	Project ID (uses default)
`-n, --display-id`	Subject display ID (required for create)
`-P, --property`	Property key=value (repeatable)
`-t, --tag`	Tag (repeatable)
`--curl`	Output curl command

Model properties: sex, date_of_birth, external_id, diagnosis, clinical_notes

iflow subjects create --display-id "SUB-001" -P sex=female -P first_name=Jane -P surname=Doe
iflow subjects get SUBJECT_ID

Samples¶

Guide: Managing Samples

Command	Description
`iflow samples list`	List samples
`iflow samples create --subject-id ID -n DISPLAY_ID`	Create sample
`iflow samples get ID`	Get sample details
`iflow samples delete ID`	Delete sample
`iflow samples sampleinfo ID`	Generate pipeline JSON

Option	Description
`-p, --project`	Project ID (uses default)
`--subject-id`	Parent subject ID (required for create)
`-n, --display-id`	Sample display ID (required for create)
`-P, --property`	Property key=value (repeatable)
`-t, --tag`	Tag (repeatable)
`--order-id`	Order ID (for sampleinfo)
`--curl`	Output curl command

Model properties: sample_type, external_id, barcode, tissue, collection_date, notes

iflow samples create --subject-id SUBJ_ID -n "NA12878" -P sample_type=germline
iflow samples sampleinfo SAMPLE_ID

Orders¶

Guide: Order Management

Command	Description
`iflow orders list`	List orders
`iflow orders create -n DISPLAY_ID`	Create order
`iflow orders get ID`	Get order details
`iflow orders transition ID STATUS`	Change status
`iflow orders delete ID`	Delete order
`iflow orders samples ID`	List samples in order
`iflow orders add-sample ORDER SAMPLE`	Add sample to order
`iflow orders remove-sample ORDER SAMPLE`	Remove sample
`iflow orders samplesheet ID`	Generate nf-core CSV

Option	Description
`-p, --project`	Project ID (uses default)
`-n, --display-id`	Order display ID (required for create)
`--accession`	Lab accession number
`--priority`	routine, urgent, stat
`--indication`	Clinical indication
`-t, --tag`	Tag (repeatable)
`--curl`	Output curl command

Statuses: created → analyzing → reviewed → signed_off → completed (+ amended, cancelled)

iflow orders create -n "Case-001" --priority urgent
iflow orders list --status created
iflow orders transition ORDER_ID analyzing
iflow orders samplesheet ORDER_ID > samplesheet.csv

Global Options¶

Option	Description
`--version`	Show CLI version
`--help`	Show help

API Debugging¶

Most commands support --curl to output the equivalent curl command:

iflow pipelines list --curl
iflow orders create -n "Test-001" --curl
iflow analyses submit --pipeline wdl-minimal --curl

Environment Variables¶

Variable	Description
`IFLOW_TOKEN`	Personal Access Token for auth
`IFLOW_FILE_URL`	File service URL
`IFLOW_COMPUTE_URL`	Compute service URL
`IFLOW_ADMIN_URL`	Admin service URL
`IFLOW_MINER_URL`	Miner service URL

Getting Help¶

iflow --help
iflow config --help
iflow analyses submit --help