Meta Tests

tests/meta/README.md

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+# Meta Tests
+
+Minimal Proof of Concept to run nf-test on Tower.
+
+Mainly for testing modules with full sized data(the stuff that really ends up breaking it) for optimization.
+
+So we thought what if we wrap nf-test in a Nextflow process, and then let it test the module?
+
+Then we could spin all of the tests up, and even get snapshots out of full test-data
+
+It's a Nextflow workflow that wraps nf-test, which itself wraps Nextflow.

tests/meta/main.nf

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+// TODO What if we took nf-test list?
+params.module_dir = "./modules/nf-core/samtools/view"
+params.repo = "../modules/"
+params.nftest_config = "./tests/meta/nf-test.config"
+params.nextflow_config = "./tests/meta/nf.config"
+
+
+workflow {
+    NFTEST_MODULE (
+        file(params.module_dir + "/main.nf"),
+        file(params.module_dir + "/tests"),
+        file(params.nftest_config),
+        file(params.nextflow_config),
+        [], // TODO
+        false
+    )
+}
+
+process NFTEST_MODULE {
+    tag "$module_file"
+
+    input:
+    path module_file
+    path test_file
+    path nftest_config
+    path nextflow_config
+    path full_repo // optional for subworkflow
+    val update_snapshot
+
+    output:
+    path "*.snap", emit: snapshot, optional: true
+
+    script:
+    def snapshot = update_snapshot ? '--update-snapshot': ''
+    """
+    # TODO cd $full_repo
+    nf-test test tests/*.nf.test \\
+        --profile docker \\
+        $snapshot \\
+        --silent \\
+        --verbose \\
+        -c $nftest_config
+    """
+}

tests/meta/nf-test.config

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+config {
+    // location for all nf-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 "nf.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile ""
+}

tests/meta/nf.config

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+params {
+    publish_dir_mode = "copy"
+    singularity_pull_docker_container = false
+    test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+}
+
+process {
+    cpus = 2
+    memory = 3.GB
+    time = 2.h
+}
+
+profiles {
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+    }
+    conda {
+        conda.enabled = true
+    }
+    mamba {
+        conda.enabled  = true
+        conda.useMamba = true
+    }
+    podman {
+        podman.enabled = true
+        podman.userEmulation = true
+        podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+    }
+    docker {
+        docker.enabled = true
+        docker.userEmulation = false
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+}
+
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Increase time available to build Conda environment
+conda { createTimeout = "120 min" }
+
+// Load test_data.config containing paths to test data
+includeConfig 'https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config'
+
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}