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 debug-level logging

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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 0.1.0 — Bioinformatics Pipeline Engine
✓ Created new project at my-pipeline
  my-pipeline/my-pipeline.oxoflow
  my-pipeline/envs/
  my-pipeline/scripts/
  my-pipeline/.gitignore

  Edit my-pipeline/my-pipeline.oxoflow to define your pipeline.

Generated files

<name>.oxoflow — Starter workflow file:

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

[config]
# Add your configuration variables here

[defaults]
threads = 4
memory = "8G"

# Define your pipeline rules below:
# [[rules]]
# name = "step1"
# input = ["input.txt"]
# output = ["output.txt"]
# shell = "cat input.txt > output.txt"

envs/ — Directory for conda YAML / Docker / Pixi environment specs.

scripts/ — Directory for helper scripts.

.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, files are written into it without overwriting existing files
• The generated .gitignore includes common bioinformatics file types and oxo-flow internal directories