nf-test.config

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"

    // ignore tests coming from the nf-core/modules repo
    // Also ignore sentieon/parabricks tests when respective env vars are set (forks/ARM/CPU-only)
    def skipSentieon = System.getenv("SKIP_SENTIEON") == "true"
    def skipParabricks = 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 parabricksTests = ['tests/parabricks_default.nf.test', 'subworkflows/local/align_star/tests/main.parabricks.nf.test', 'subworkflows/local/prepare_genome/tests/main.parabricks.nf.test']

    ignore = baseIgnore + (skipSentieon ? sentieonTests : []) + (skipParabricks ? parabricksTests : [])

    // run all tests with the profile(s) specified by each CI workflow

    // 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"
    }
}