`oxo-flow init`#

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

Usage#

oxo-flow init [OPTIONS] <NAME>

Arguments#

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

Options#

Option	Short	Default	Description
`--dir`	`-d`	`./<NAME>`	Output directory (defaults to the project name)
`--verbose`	`-v`	—	Enable debug-level logging

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

Output#

oxo-flow 0.6.1 — 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]
greeting = "Hello from oxo-flow!"

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

[[rules]]
name = "hello_world"
input = ["data/input.txt"]
output = ["results/output.txt"]
shell = "echo '{config.greeting}' > {output[0]} && cat {input[0]} >> {output[0]}"

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

scripts/ — Directory for helper scripts.

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).

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

oxo-flow init#