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test command

Usage

nf-test test [<NEXTFLOW_FILES>|<SCRIPT_FOLDERS>]

Optional Arguments

--profile <NEXTFLOW_PROFILE>

To run your test using a specific Nextflow profile, you can use the --profile argument. Learn more.

--dry-run

This flag allows users to simulate the execution of tests.

--verbose

Prints out the Nextflow output during test runs.

--without-trace

The Linux tool procps is required to run Nextflow tracing. In case your container does not support this tool, you can also run nf-test without tracing. Please note that the workflow.trace are not available when running it with this flag.

--tag <tag>

Execute only tests with the provided tag. Multiple tags can be used and have to be separated by commas (e.g. tag1,tag2).

--debug

The debug parameter prints out debugging messages and all available output channels which can be accessed in the then clause.

Output Reports

--tap <filename>

Writes test results in TAP format to file.

--junitxml <filename>

Writes test results in JUnit XML format to file, which conforms to the standard schema.

--csv <filename>

Writes test results in csv file.

--ci

By default,nf-test automatically stores a new snapshot. When CI mode is activated, nf-test will fail the test instead of storing the snapshot automatically.

--filter <types>

Filter test cases by specified types (e.g., module, pipeline, workflow or function). Multiple types can be separated by commas.

Optimizing Test Execution

--related-tests <files>

Finds and executes all related tests for the provided .nf or nf.test files. Multiple files can be provided space separated.

--follow-dependencies

When this flag is set, nf-test will traverse all dependencies when the related-tests flag is set. This option is particularly useful when you need to ensure that all dependent tests are executed, bypassing the firewall calculation process.

--only-changed

When enabled, this parameter instructs nf-test to execute tests only for files that have been modified within the current git working tree.

--changed-since <commit_hash|branch_name>

This parameter triggers the execution of tests related to changes made since the specifie commit. e.g. --changed-since HEAD^ for all changes between the HEAD and HEAD - 1.

--changed-until <commit_hash|branch_name>

This parameter initiates the execution of tests related to changes made until the specified commit hash.

--graph <filename>

Enables the export of the dependency graph as a dot file. The dot file format is commonly used for representing graphs in graphviz and other related software.

Sharding

This parameter allows users to divide the execution workload into manageable chunks, which can be useful for parallel or distributed processing.

--shard <shard>

Splits the execution into arbitrary chunks defined by the format i/n, where i denotes the index of the current chunk and n represents the total number of chunks. For instance, 2/5 executes the second chunk out of five.

--shard-strategy <strategy>

Description: Specifies the strategy used to build shards when the --shard parameter is utilized. Accepted values are round-robin or none.. This parameter determines the method employed to distribute workload chunks among available resources. With the round-robin strategy, shards are distributed evenly among resources in a cyclic manner. The none strategy implies that shards won't be distributed automatically, and it's up to the user to manage the assignment of shards. Default value is round-robin.

Examples

  • Run all test scripts that can be found in the testDir defined in the nf-test.config file in the current working directory:
nf-test test
  • Run all specified test scripts and search specified directories for additional test scripts:
nf-test test tests/modules/local/salmon_index.nf.test tests/modules/bwa_index.nf.test

nf-test test tests/modules tests/modules/bwa_index.nf.test
  • Run a specific test using its hash:
nf-test test tests/main.nf.test@d41119e4
  • Run all tests and write results to report.tap:
nf-test test --tap report.tap
  • Run all tests (and possible integration tests) for module modules/module_a.nf and modules/module_b.nf;
nf-test test --related-tests modules/module_a.nf modules/module_b.nf
  • If your project is a Git directory and you have modified files, you can run tests only for these changed files by using the following command:
nf-test test --only-changed
  • If you want to test all changes made between the current state of the repository and the last commit, you can use the following command:
nf-test test --changed-since HEAD^
  • Run only the second of four shards:
nf-test test --shard 2/4