Testing nf-core/modules
Edit

Writing comprehensive tests for nf-core modules with nf-test

Overview

The nf-test framework in the nf-core ecosystem enables comprehensive testing for processes, workflows, and pipelines.

This chapter covers the fundamentals of nf-core module testing, from basic syntax to advanced scenarios involving chained modules.

Basic test syntax

The basic syntax for a process test follows this structure:

nextflow_process {
    name "<NAME>"
    script "<PATH/TO/NEXTFLOW_SCRIPT.nf>"
    process "<PROCESS_NAME>"
 
    test("<TEST_NAME>") {
        // Test implementation
    }
}

Note

Key points:

Script paths starting with ./ or ../ are relative to the test script’s location.

Essential Assertions

Tests use assertions to verify the expected output of the process in the then block.

To report multiple failures in a single test run, group your assertions within an assertAll block.

Channels that lack explicit names can be addressed using square brackets and the corresponding index, for example process.out[0] for the first channel. This indexing method provides a straightforward way to interact with channels without the need for predefined names.

// Process status
assert process.success
assert process.exitStatus == 0
 
// Output channels
assert process.out.my_channel != null
assert process.out.my_channel.size() == 3
assert process.out.my_channel.get(0) == "expected_value"
 
// For unnamed channels, use index notation
assert process.out[0] != null
assert process.out[0].size() == 3
 
// Group assertions to see all failures at once
assertAll(
    { assert process.success },
    { assert snapshot(process.out).match() }
)

Module testing principles

Each module should contain a tests/ folder alongside its main.nf file.
Test files come with snapshots of component output channels (a stored representation of the correct channel contents).
Tests verify both functionality and expected outputs.
Support both regular and stub (-stub) testing modes.

Testing an existing module

Let’s examine testing the bedtools/bamtobed module, which is a simple standalone module:

cd path/to/modules
# Run all tests for the module
nf-core modules test bedtools/bamtobed --profile docker

This will run all tests for the module and display the results, including any failures or snapshot mismatches.

 
 
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'
 
    nf-core/tools version 3.3.2 - https://nf-co.re
 
 
INFO     Generating nf-test snapshot
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process BEDTOOLS_BAMTOBED                                                                         │
│                                                                                                        │
│   Test [824188d1] 'sarscov2 - bam' PASSED (3.335s)                                                     │
│   Test [f4f6429b] 'stub' PASSED (3.154s)                                                               │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 2 tests in 6.498s                                                                    │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process BEDTOOLS_BAMTOBED                                                                         │
│                                                                                                        │
│   Test [824188d1] 'sarscov2 - bam' PASSED (3.277s)                                                     │
│   Test [f4f6429b] 'stub' PASSED (3.161s)                                                               │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 2 tests in 6.446s                                                                    │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed!

Creating a new module with tests

When creating a new module using nf-core/tools, a test file is automatically generated based on the template.

# Create a new module using nf-core/tools
cd path/to/modules
nf-core modules create seqtk/sample

This creates the following module structure:

modules/nf-core/seqtk/sample/
├── main.nf
├── meta.yml
└── tests/
    ├── main.nf.test
    └── tags.yml

The generated test file (tests/main.nf.test), with positional input channels input[0] and input[1] provided, will look like this:

nextflow_process {
 
    name "Test Process SEQTK_SAMPLE"
    script "../main.nf"
    process "SEQTK_SAMPLE"
 
    tag "modules"
    tag "modules_nfcore"
    tag "seqtk"
    tag "seqtk/sample"
 
    test("sarscov2 - fastq") {
 
        when {
            process {
                """
                input[0] = [
                    [ id:'test', single_end:false ], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                ]
                input[1] = 10  // Number of reads to sample
                """
            }
        }
 
        then {
            assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
        }
    }
 
    test("sarscov2 - fastq - stub") {
 
        options "-stub"
 
        when {
            process {
                """
                input[0] = [
                    [ id:'test', single_end:false ], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                ]
                input[1] = 10
                """
            }
        }
 
        then {
            assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
        }
    }
}

After providing the appropriate test data, run the tests to create a snapshot of the output:

nf-core modules test seqtk/sample --profile docker

 
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'
 
    nf-core/tools version 3.3.2 - https://nf-co.re
 
 
INFO     Generating nf-test snapshot
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process SEQTK_SAMPLE                                                                              │
│                                                                                                        │
│   Test [a4edc395] 'sarscov2_sample_singleend_fqgz' PASSED (14.223s)                                    │
│   Test [42c1ef08] 'sarscov2_sample_pairedend_fqgz' PASSED (3.353s)                                     │
│   Test [7b327705] 'sarscov2_sample_singlend_fqgz_stub' PASSED (3.042s)                                 │
│   Test [f1c40b60] 'sarscov2_sample_singleend_frac' PASSED (3.326s)                                     │
│                                                                                                        │
│ Test Workflow FASTQ_CONTAM_SEQTK_KRAKEN                                                                │
│                                                                                                        │
│   Test [609e9434] 'sarscov2 - fastq - 25000 - krakendb' PASSED (31.378s)                               │
│   Test [b5fb1cc0] 'sarscov2 - fastq - [12500, 25000] - krakendb' PASSED (7.803s)                       │
│   Test [aac34908] 'sarscov2 - fastq - [12500, 25000] - krakendb -- stub' PASSED (7.262s)               │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 7 tests in 70.391s                                                                   │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process SEQTK_SAMPLE                                                                              │
│                                                                                                        │
│   Test [a4edc395] 'sarscov2_sample_singleend_fqgz' PASSED (3.611s)                                     │
│   Test [42c1ef08] 'sarscov2_sample_pairedend_fqgz' PASSED (3.321s)                                     │
│   Test [7b327705] 'sarscov2_sample_singlend_fqgz_stub' PASSED (3.098s)                                 │
│   Test [f1c40b60] 'sarscov2_sample_singleend_frac' PASSED (3.263s)                                     │
│                                                                                                        │
│ Test Workflow FASTQ_CONTAM_SEQTK_KRAKEN                                                                │
│                                                                                                        │
│   Test [609e9434] 'sarscov2 - fastq - 25000 - krakendb' PASSED (5.934s)                                │
│   Test [b5fb1cc0] 'sarscov2 - fastq - [12500, 25000] - krakendb' PASSED (6.564s)                       │
│   Test [aac34908] 'sarscov2 - fastq - [12500, 25000] - krakendb -- stub' PASSED (7.03s)                │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 7 tests in 32.853s                                                                   │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed!

Testing parameter variations

There are two primary ways to alter parameters for a module test: creating a test-specific configuration file or using a params block within the test itself.

Creating a parameter-specific configuration

For modules requiring additional parameters, you can create a <filename>.config file in the tests/ directory:

# Create config file for parameter testing
touch modules/nf-core/seqtk/sample/tests/nextflow.config

Add the configuration:

process {
    withName: 'SEQTK_SAMPLE' {
        ext.args = params.module_args
    }
}

Then apply the config in your test as shown below:

nextflow_process {
    name "Test Process SEQTK_SAMPLE"
    script "../main.nf"
    process "SEQTK_SAMPLE"
    config "./nextflow.config"
 
    test("pass module_args to the module") {
        when {
            params {
                module_args = "--help"
            }
            process {
                """
                input[0] = [
                    [ id:'test', single_end:false ], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                ]
                input[1] = 10
                """
            }
        }
        then {
            // ...
        }
    }
}

Overriding parameters with the `params` block

In addition to a nextflow.config file, nf-test provides a params block within the when block to override Nextflow’s input params for a specific test.

when {
  params {
    outdir = "output"
  }
  process {
    """
    input[0] = [
      [ id:'test', single_end:false ], // meta map
      file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
    ]
    input[1] = 10
    """
  }
}

Testing chained modules

For modules that depend on the output of other modules, use the setup method to define the dependency.

The setup method allows you to specify processes or workflows that need to be executed before the primary when block. It serves as a mechanism to prepare the required input data or set up essential steps prior to the primary processing block.

Within the setup block, you can use the run method to define and execute dependent processes or workflows.

Syntax

The run method syntax for a process is as follows:

run("ProcessName") {
    script "path/to/process/script.nf"
    process {
        // Define the process inputs here
    }
}

The run method syntax for a workflow is as follows:

run("WorkflowName") {
    script "path/to/workflow/script.nf"
    workflow {
        // Define the workflow inputs here
    }
}

Warning

Please keep in mind that changes in processes or workflows, which are executed in the setup method, can result in a failed test run.

Local `setup` method

A setup method can be defined within a test case to execute a dependent process. This process generates input data required for the primary process. The setup block specifies the execution of the dependency, and the when block defines the processing logic for the module under test.

Here’s an example for abricate/summary, which requires output from abricate/run:

nextflow_process {
 
    name "Test Process ABRICATE_SUMMARY"
    script "../main.nf"
    process "ABRICATE_SUMMARY"
 
    tag "modules"
    tag "modules_nfcore"
    tag "abricate"
    tag "abricate/summary"
 
    test("bacteroides_fragilis - genome_fna_gz") {
 
        setup {
            run("ABRICATE_RUN") {
                script "../../run/main.nf"
                process {
                    """
                    input[0] = Channel.fromList([
                        tuple([ id:'test1', single_end:false ], // meta map
                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)),
                        tuple([ id:'test2', single_end:false ],
                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true))
                    ])
                    """
                }
            }
        }
 
        when {
            process {
                """
                // Collect reports from ABRICATE_RUN, create a new meta map, and provide it as input
                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
                """
            }
        }
 
        then {
            assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
        }
    }
}

Run the tests:

nf-core modules test abricate/summary --profile docker

This will execute the test with the chained module setup, running ABRICATE_RUN first to generate the required input, then testing ABRICATE_SUMMARY with that output.

 
 
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'
 
    nf-core/tools version 3.3.2 - https://nf-co.re
 
 
INFO     Generating nf-test snapshot
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process ABRICATE_SUMMARY                                                                          │
│                                                                                                        │
│   Test [fc133477] 'Should run without failures' PASSED (102.456s)                                      │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 1 tests in 102.459s                                                                  │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability
╭──────────────────────────────────────────── nf-test output ────────────────────────────────────────────╮
│                                                                                                        │
│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│                                                                                                        │
│ Test Process ABRICATE_SUMMARY                                                                          │
│                                                                                                        │
│   Test [fc133477] 'Should run without failures' PASSED (11.658s)                                       │
│                                                                                                        │
│                                                                                                        │
│ SUCCESS: Executed 1 tests in 11.667s                                                                   │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed!

Global `setup` method

A global setup method can be defined for all tests within a nextflow_process definition. The setup is applied to multiple test cases, ensuring a consistent setup for each test. This approach is useful when multiple tests share the same setup requirements.

nextflow_process {
 
    name "Test Process ABRICATE_SUMMARY"
    script "../main.nf"
    process "ABRICATE_SUMMARY"
    config "./nextflow.config"
 
    setup {
        run("ABRICATE_RUN") {
            script "../../run/main.nf"
            process {
                """
                input[0] =  Channel.fromList([
                    tuple([ id:'test1', single_end:false ], // meta map
                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)),
                    tuple([ id:'test2', single_end:false ],
                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true))
                ])
                """
            }
        }
    }
 
    test("first test") {
        when {
            process {
                """
                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
                """
            }
        }
        then {
            assert process.success
            assert snapshot(process.out).match()
        }
    }
 
    test("second test") {
        when {
            process {
                """
                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
                """
            }
        }
        then {
            assert process.success
            assert snapshot(process.out).match()
        }
    }
}

Aliasing dependencies

If you need to run the same process multiple times, you can set an alias for the process:

nextflow_process {
 
    // ...
 
    setup {
 
        run("UNTAR", alias: "UNTAR1") {
            script "modules/nf-core/untar/main.nf"
            process {
            """
            input[0] = Channel.fromList(...)
            """
            }
        }
 
        run("UNTAR", alias: "UNTAR2") {
            script "modules/nf-core/untar/main.nf"
            process {
            """
            input[0] = Channel.fromList(...)
            """
            }
        }
 
        run("UNTAR", alias: "UNTAR3") {
            script "modules/nf-core/untar/main.nf"
            process {
            """
            input[0] = Channel.fromList(...)
            """
            }
        }
    }
 
    test("Test with three different inputs") {
        when {
            process {
                """
                input[0] = UNTAR1.out.untar.map{ it[1] }
                input[1] = UNTAR2.out.untar.map{ it[1] }
                input[2] = UNTAR3.out.untar.map{ it[1] }
                """
            }
        }
 
        then {
            // ...
        }
    }
}

Updating module snapshots

When module outputs change (e.g., due to version bumps), you need to update snapshots:

nf-core modules test abricate/summary --profile docker --update

You will see the following warning at the start of the test run:

│ 🚀 nf-test 0.9.0                                                                                       │
│ https://www.nf-test.com                                                                                │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                   │
│                                                                                                        │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                  │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                        │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                  │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                  │
│ Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar                                              │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                              │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                          │
│ Warning: every snapshot that fails during this test run is re-record.

Once the test passes, the snapshot will be updated and the test re-run to verify the snapshot is stable.

Testing with nf-test

You can also run the tests with nf-test directly using the --tag option:

nf-test test --profile docker --tag abricate/summary
 
# or specify test path
nf-test test --profile docker modules/nf-core/abricate/summary/tests/main.nf.test

This will run the tests for the module and display the results, including any failures or snapshot mismatches.

🚀 nf-test 0.9.0
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr
 
Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar
Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar
Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar
Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar
Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar
 
Test Process ABRICATE_SUMMARY
 
  Test [fc133477] 'Should run without failures' PASSED (15.286s)
 
 
SUCCESS: Executed 1 tests in 15.294s

Note

The nf-test test command runs the test only once compared to the nf-core modules test command which runs the test twice to confirm snapshot stability.

Note

For more nf-test assertion patterns, see the nf-test assertions examples documentation.

Next steps

Continue to Testing Subworkflows to learn about testing more complex multi-module components.

Testing nf-core/modules Edit

Overview

Basic test syntax

Essential Assertions

Module testing principles

Testing an existing module

Creating a new module with tests

Testing parameter variations

Creating a parameter-specific configuration

Overriding parameters with the params block

Testing chained modules

Syntax

Local setup method

Global setup method

Aliasing dependencies

Updating module snapshots

Testing with nf-test

Next steps

Testing nf-core/modules
Edit

Overriding parameters with the `params` block

Local `setup` method

Global `setup` method