oxo-flow init

Initialize a new workflow project with a starter .oxoflow file, directory structure, and .gitignore.

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Usage

oxo-flow init [OPTIONS] <NAME>

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Arguments

Argument	Description
<NAME>	Project name (also used as the default directory name)

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Options

Option	Short	Default	Description
--dir	-d	./<NAME>	Output directory (defaults to the project name)
--verbose	-v	—	Enable verbose (debug-level) logging
--quiet	—	—	Suppress non-essential output (errors only)
--no-color	—	—	Disable colored output
--json	—	—	Output machine-readable JSON to stdout

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Examples

Create a new project

oxo-flow init my-pipeline

Create in a specific directory

oxo-flow init my-pipeline -d /projects/genomics/my-pipeline

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Output

oxo-flow v0.15.0 — Rust-native bioinformatics pipeline engine
✓ Created new project at my-pipeline
  my-pipeline/my-pipeline.oxoflow
  my-pipeline/envs/example.yaml
  my-pipeline/scripts/example.sh
  my-pipeline/.gitignore

  Next steps: To run your first workflow:
    cd my-pipeline
    oxo-flow run my-pipeline.oxoflow

Generated files

<name>.oxoflow — Starter workflow file:

[workflow]
name = "my-pipeline"
version = "0.1.0"
description = "A new oxo-flow pipeline"
author = ""

[config]
# Variables defined here are used in shell commands as {config.key}
sample_name = "example"
greeting = "Hello from oxo-flow!"

[defaults]
threads = 1
memory = "1G"

[[rules]]
name = "hello_world"
description = "A minimal rule that writes a greeting"
output = ["results/{config.sample_name}_output.txt"]
shell = "echo '{config.greeting}' > {output[0]}"

envs/example.yaml — Starter conda environment specification.

scripts/example.sh — Starter helper script.

data/ — Pre-populated with an input.txt sample to allow immediate execution.

results/ — Empty directory created for workflow outputs.

.gitignore — Pre-configured with bioinformatics patterns (BAM, VCF, index files, workflow outputs).

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Notes

• The output directory is created if it does not exist
• If the directory already exists, oxo-flow prints a warning and files may be overwritten
• The generated .gitignore includes common bioinformatics file types and oxo-flow internal directories