Resources for testing

Request for more test resources

Test runners are tailored to restrain their resources usage to specifically what is asked for by Nextflow through the configuration files. For nf-neuro tests, you can find this configuration in tests/config/nextflow.config. If any of your tests ask for more, you need to define it correctly.

Note

The container detects out-of-bound resource consumption automatically, tests will fail if they haven’t been assigned them sufficiently. It’s a good way to catch them.

First, resource requirements need to be defined in the nextflow.config file(s) of your test cases. Add the process.cpu and process.memory and set their requirements as needed :

process.memory = '9G'
process.cpus = 6

or

process {
  memory = '10G'
  cpus = 6
}

To allow test runners on your PR to run with sufficient resources, you’ll need to specify to which class of runners to assign to. To do so, edit .github/workflows/run_checks_suite.yml. Find the matrix definition for the nf-test job (currently around line 133) and add the following request for a runner in the include section :

- runner: <name-of-the-runner-class>
  path: modules/nf-neuro/<category>/<tool>

Available runner classes that superseed default :

Runner Class	Resources
(default)	4 CPU 4Gb RAM
scilus-nf-neuro-bigmem-runners	16Gb RAM

Caution

Specialized runners are limited !!! They are allocated for hungry processes, such as AI/ML models and large dataset studies, don’t abuse them. The more they are requested for, the longer PR take to merge, so don’t ask for them for nothing, meaning be smart in designing your modules ! PRs deemed not needing them will be automatically closed.