nf-test

nf-test Testing

Run and manage tests using nf-test for Nextflow pipelines and modules.

Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for nf-core conventions and package manager setup. Read ${CLAUDE_PLUGIN_ROOT}/shared/test-patterns.md for test templates and patterns.

---

Quick Commands

Replace <cmd> with the configured package manager prefix (see Setup in conventions.md).

<cmd> nf-test test                                # Run all tests
<cmd> nf-test test tests/modules/fastqc/           # Specific path
<cmd> nf-test test --profile +docker               # Add container profile (+ ADDS, no + REPLACES)
<cmd> nf-test test --tag "modules"                  # Filter by tag
<cmd> nf-test test --update-snapshot                # Update snapshots
<cmd> nf-test test --verbose                        # Verbose output
<cmd> nf-test list                                  # List available tests

---

Process Tests

nextflow_process {
    name "Test Process FASTQC"
    script "../main.nf"
    process "FASTQC"

    tag "modules"
    tag "fastqc"

    test("Single-end reads") {
        when {
            process {
                """
                input[0] = [
                    [ id:'test', single_end:true ],
                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
                ]
                """
            }
        }
        then {
            assert process.success
            assert snapshot(process.out).match()
        }
    }

    test("Stub run") {
        options "-stub"
        when {
            process {
                """
                input[0] = [ [ id:'test' ], file('dummy.fastq.gz') ]
                """
            }
        }
        then {
            assert process.success
            assert snapshot(process.out).match()
        }
    }
}

---

Pipeline-Level Tests

Pipeline tests use nextflow_pipeline (NOT nextflow_workflow) and load params via profiles. Params are NEVER defined inline — they go in conf/test_XYZ.config.