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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 (scripts and report templates — 09_single_cell_rnaseq, 11_conditional_workflow, 14_paired_experiment_control, 15_paired_experiment_control_pairs) copy them next to the generated workflow, so the generated pipeline is immediately complete and runnable.

Options#

Option Description
-o, --output <OUTPUT> Output file or directory (a trailing slash forces a directory, created if missing). Defaults to current directory with template name
--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)

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

See Also#