oxo-flow template#

Generate a workflow from a predefined gallery template.

Usage#

oxo-flow template [OPTIONS] [TEMPLATE]

Description#

Lists available templates when called without arguments. When a template name is provided, generates a .oxoflow file based on that template, substituting the workflow name appropriately.

Templates are drawn from the Workflow Gallery and range from a one-rule hello-world to production-grade multi-omics pipelines. The gallery is embedded in the binary at build time, so it works identically whether oxo-flow is installed from a release or run from a source checkout.

Templates that reference auxiliary files copy them next to the generated workflow, so the generated pipeline is immediately complete and runnable. This covers report scripts and report templates (09_single_cell_rnaseq, 11_conditional_workflow, 14_paired_experiment_control, 15_paired_experiment_control_pairs) as well as the conda environment definitions referenced by conda = "envs/..." in templates 04-15.

Options#

Option	Description
`-o, --output <OUTPUT>`	Output file or directory (a trailing slash forces a directory, created if missing). Defaults to the current directory with the template's name minus its numeric prefix (e.g. `01_hello_world` → `hello_world.oxoflow`)
`--ai`	Generate the workflow with AI from a natural language description
`--from-url <URL>`	URL(s) to use as reference material for AI generation (repeatable)
`--from-file <PATH>`	File(s) to use as reference material for AI generation (repeatable)
`--ai-max-retries <N>`	Maximum AI correction rounds (overrides config)
`--ai-team-profile <PROFILE>`	Generation team profile: `compact` (one agent + engine gates, default) or `full` (adds the task contract, the deterministic Curator brief, and an independent review pass with a bounded fix). Overrides `[ai] team_profile` in the config
`--ai-attempts <N>`	Fresh-draw attempts for the whole generation (best-of-N: up to N independent tries; the first one passing the deterministic gates wins, so later attempts are only paid when earlier ones fail) [default: 1]

Examples#

# List all available templates
oxo-flow template

# Generate the hello-world template in the current directory
oxo-flow template 01_hello_world

# Generate to a specific file
oxo-flow template 06_rnaseq_quantification -o my_rnaseq.oxoflow

# Generate into a specific directory  
oxo-flow template 07_wgs_germline -o projects/wgs/

Available Templates#

Name	Description
`01_hello_world`	Minimal single-rule workflow
`02_file_pipeline`	Linear three-step file processing
`03_parallel_samples`	Parallel sample processing with wildcards
`04_scatter_gather`	Chromosome-based scatter-gather pattern
`05_conda_environments`	Multi-environment workflow
`06_rnaseq_quantification`	RNA-seq quantification pipeline
`07_wgs_germline`	WGS germline variant calling
`08_multiomics_integration`	Multi-omics integration
`09_single_cell_rnaseq`	Single-cell RNA-seq processing
`10_transform_operator`	Transform operator demo
`11_conditional_workflow`	Conditional execution
`12_cohort_analysis`	Cohort-level QC aggregation
`13_simple_variant_calling`	Simple germline variant calling
`14_paired_experiment_control`	Somatic variant calling (single pair)
`15_paired_experiment_control_pairs`	Somatic variant calling (multiple pairs)
`16_16s_qiime2_amplicon`	16S amplicon analysis with QIIME2