CLI

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 process [config.toml]  [--allow-overwrite]
mbf-fastq-processor template
mbf-fastq-processor interactive [config.toml]

Process #

Process FASTQ as described in <config.toml>.(see the TOML format reference). Relative paths are resolved against the current shell directory.

The config.toml argument can be left off iff there’s one .toml in the current directory, and it contains an [input] and an [output] section

(not) “Done” marker file #

By default, existence of any output file will lead to an early abort, before any processing happens (other output files might have been created with 0 bytes at this point though). If you pass –allow-overwrite (or if an output.incomplete file exists), existing output files are overwritten instead.

The output.incomplete file exists until the successful exit of mbf-fastq-processor. This way you can detect incomplete runs by the existence of that file.

Behaviour #

  • Exit status 0 denotes success; non-zero exit codes indicate configuration, IO, or data validation failures.
  • Error messages go to stderr. Helpful hints for configuration issues also go to stderr.
  • –help goes to stdout. Run without arguments shows help, going to stderr.
  • by default there is no stdout output. Progress can change that.

Template #

Output a configuration file showing all the options, ready to be ‘uncommented’.

The template is also available here.

Appropriate parts of the template are also shown when a configuration error is detected.

Interactive #

The interactive mode takes your configuration file, samples 15 from the first 10,000 reads (configurable via CLI arguments), and shows you the Inspect results.

Every time you save, the results refresh.

This way you can quickly tune and work on your configuration.

Development with Cargo #

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

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

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.