config {

// location for all nf-test tests

testsDir = "."

// nf-test directory including temporary files for each test

workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"

// location of an optional nextflow.config file specific for executing tests

configFile = "tests/nextflow.config"

// Also ignore sentieon/GPU tests when respective env vars are set (forks/ARM/CPU-only)

def skipSentieon = System.getenv("SKIP_SENTIEON") == "true"

def skipGpu = System.getenv("SKIP_GPU") == "true" || System.getenv("SKIP_PARABRICKS") == "true"

def baseIgnore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']

def sentieonTests = ['tests/sentieon_default.nf.test', 'subworkflows/local/align_star/tests/main.sentieon.nf.test']

def gpuTests = ['tests/parabricks_default.nf.test', 'tests/gpu_ribodetector.nf.test', 'subworkflows/local/align_star/tests/main.parabricks.nf.test', 'subworkflows/local/prepare_genome/tests/main.parabricks.nf.test']

ignore = baseIgnore + (skipSentieon ? sentieonTests : []) + (skipGpu ? gpuTests : [])

// Note: no `profile "test"` here — this is intentional. The pipeline supports both

// CPU (`test`) and GPU (`test_gpu`) profiles with different resource limits, so the

// profile is injected by each CI workflow instead. When running tests locally, you

// must include the test profile explicitly: nf-test test --profile=+test,docker

// See docs/CONTRIBUTING.md for details.

// list of filenames or patterns that should be trigger a full test run

triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore', 'modules.json']

// load the necessary plugins

plugins {

load "nft-bam@0.4.0"

load "nft-utils@0.0.5"

}

}