Command line interface #

mbf-fastq-processor is configured exclusively through a TOML document. The CLI is therefore intentionally minimal and focuses on selecting the configuration and the working directory.

Usage #

mbf-fastq-processor <config.toml> [working_directory]

• config.toml – required path to the pipeline description (see the TOML format reference). Relative paths are resolved against the current shell directory.
• working_directory – optional override for the process working directory. Use it to anchor relative paths inside the configuration without changing your shell location.

When working_directory is omitted, the binary inherits the environment’s current directory.

Behaviour #

• Exit status 0 denotes success; non-zero exit codes indicate configuration, IO, or data validation failures.
• Log output is emitted on stderr. Enable structured logging with RUST_LOG=info (or debug) when troubleshooting.
• The process honours OS-level resource limits and can be composed in scripts or pipelines; the FastQ stream on stdout is available when [output] sets stdout = true.

Working with Cargo #

During development you can run the CLI straight from the workspace:

cargo run --release -- path/to/config.toml

Cargo passes -- through to the binary; add the optional working directory argument if needed. For faster iteration without full optimisation use cargo run --.

If your configuration only defines [input] and [output], the processor behaves much like a decompression-aware cat, copying reads while honouring the configured compression format.