Getting started with development #

The easiest way to get started with working on mbf-fastq-processor is to clone the repository:

jj git clone --colocate https://github.com/TyberiusPrime/mbf-fastq-processor

or

git clone  https://github.com/TyberiusPrime/mbf-fastq-processor

if you’re not yet convinced that Jujutsu is the better git.

Development environment #

Using nix develop to enter a shell with all the necessary requirements using Nix.

If you don’t use nix, you’re on your own to supply a matching rust compiler, openssl and pkg-config.

Development with Cargo #

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

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

–release is optional, but cargo debug builds can be slow.

See the CLI documentation for arguments after the -- that splits the cargo run arguments from the process arguments.

Running tests #

Run all tests #

cargo test 

Run a specific test #

cargo test <test-name-substring> 

Run from a test_case folder #

cargo run -- verify 

Benchmarking #

bash cargo bench

will get you a (not so) quick benchmark of our individual components.

Manipulating core count #

In addition to the config options in the input-section or in the Options section, you can influence the number of cores used for the automatic decisions on thread counts by setting the MBF_FASTQ_PROCESSOR_NUM_CPUS environment variable.