`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 (no path separators; 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 verbose (debug-level) logging
`--quiet`	—	—	Suppress non-essential output (errors only)
`--no-color`	—	—	Disable colored output

The global --json flag is not supported by this command — passing it fails fast instead of being silently ignored. Machine-readable output is available from: run, dry-run, validate, lint, test, status, batch, info, schema, license, ai, and provenance verify.

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 v0.23.2 — 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

All output (including the version banner) goes to stderr; the banner appears only on an interactive terminal and is suppressed by --quiet.

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"]
# The greeting is passed via the environment, not spliced into the shell —
# an apostrophe or quote in the config value cannot break the command
# (`--arg greeting=...` overrides the default).
envvars = { GREETING = "{config.greeting}" }
shell = "echo \"$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).

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

oxo-flow init#