Command line tool for automated testing of Nextflow pipelines and scripts. The tool allows for automated assertions on output files and customizable output directory settings.
pip install git+ssh://[email protected]/uclahs-cds/tool-NFTest.git
cd </path/to/cloned/repository>
pip install .
Add the NFTest badge to pipelines:
[](https://github.com/uclahs-cds/tool-NFTest)
- To initialize the testing framework, run the following in the desired directory:
nftest init
-
Define the parameters and test cases in the environment and the config files.
-
To launch the tests, run:
usage: nftest run [-h] [-c [CONFIG_FILE]] [TEST_CASES [TEST_CASES ...]]
Run nextflow tests.
positional arguments:
TEST_CASES Exact test case to run. (default: None)
optional arguments:
-h, --help show this help message and exit
-c [CONFIG_FILE], --config-file [CONFIG_FILE]
Path the the nextflow test config YAML file. If not given, it looks for nftest.yaml or nftest.yml (default: None)
nftest expects a config file named nftest.yaml or nftest.yml in the directory where the command is invoked.
To run all test cases, simply run:
nftest run
usage: nftest init [-h]
Initialize nftest by creating a nftest.yaml template.
optional arguments:
-h, --help show this help message and exit
Initialization will result in automated creation of a directory for holding test files along with an initial copy of the global configuration file and the test case YAML. These files can subsequently be populated and expanded to define the test cases.
usage: nftest run [-h] [-c [CONFIG_FILE]] [TEST_CASES [TEST_CASES ...]]
Run nextflow tests.
positional arguments:
TEST_CASES Exact test case to run. (default: None)
optional arguments:
-h, --help show this help message and exit
-c [CONFIG_FILE], --config-file [CONFIG_FILE]
Path the the nextflow test config YAML file. If not given, it looks for nftest.yaml or nftest.yml (default: None)
nftest expects a config file named nftest.yaml or nftest.yml in the directory where the command is invoked.
To run all test cases, simply run:
nftest run
To run specific test case(s), use the following command
nftest run <test name in nftest.yaml file>
Testing runs can be configured through environment variables. Theses variables can be stored in ~/.env or <current working directory>/.env in dotenv format. See template for an example. Alternatively, the variables can also be set through export (for Bash and zsh shells) in the shell prior to running the tool. The available environment variable settings are:
| Variable | Description | Default |
|---|---|---|
NFT_OUTPUT |
Output directory for parameter for Nextflow. Parameter name is designated by output_directory_param_name for each case. |
./ |
NFT_TEMP |
Temporary directory root to be used for Nextflow working files. Combined with temp_dir from global configuration to create final directory. See NXF_WORK here for details. |
./ |
NFT_INIT |
Directory where initialized files will be created. Also the directory where the tool will search for the global configuration file. | Current working directory |
NFT_LOG_LEVEL |
Python logging level. See logging levels for more details and available options. |
INFO |
NFT_LOG |
Path to file for writing log messages. By default, logging will append to file if it exists. | <NFT_OUTPUT>/log-nftest-<date>.log |
The YAML config file outlining the test cases is required to have two keys at the top level: global and cases. The global key controls global settings such as the path to the Nextflow temporary directory, global Nextflow config, and whether to remove Nextflow temporary files are each test case. The cases key contains the list of test cases. See [here]
The config file requires to have two keys at the top level, global and cases. global controls global settings such as path to the nextflow temporary dir, global nextflow config, whether to remove nextflow temporary files after each run. cases holds a list of all test cases. See here for an example.
The settings available with the global key:
| Setting | Description | Default |
|---|---|---|
temp_dir |
Directory to be added to NFT_TEMP environment variable to create Nextflow working directory. |
required |
nf_config |
Path to be added to NFT_INIT to derive global .config file for Nextflow. |
required |
remove_temp |
Whether to remove the Nextflow working directory after each case. | True |
clean_logs |
Whether to remove log files generated by Nextflow. | True |
The list of cases and settings for each case. The settings from global will be used for each case as default if specific settings for a case are not provided.
The settings available for each case:
| Setting | Description | Default |
|---|---|---|
temp_dir |
Directory to be added to NFT_TEMP environment variable to create Nextflow working directory. |
value from global |
nf_config |
Path to be added to NFT_INIT to derive global .config file for Nextflow. |
value from global |
profiles |
Ordered list of profiles to use with Nextflow through the -profile option. |
None |
remove_temp |
Whether to remove the Nextflow working directory after each case. | value from global |
clean_logs |
Whether to remove log files generated by Nextflow. | value from global |
name |
Name of the test case; used to identify the case and for selecting specific cases to run. | None |
message |
Message to display in log when running test case. | None |
nf_script |
Nextflow script to run for test case. | None |
nf_configs |
List of config file(s) to be passed to Nextflow via the -c option for nextflow run. |
[] |
params_file |
JSON or YAML file containing parameters for Nextflow script. |
None |
output_directory_param_name |
Parameter name to pass output directory to Nextflow. Passed through command line. | output_dir |
asserts |
List of assertions to make for test case. See assertions for details. | [] |
skip |
Whether to skip this test case. | False |
verbose |
Whether to capture output of nextflow run command in log. |
False |
Asserts define a list of assertions to be made for each given test case. For each case, the tool checks if a script for comparison was provided. If provided, it gets used; otherwise, the tool checks for the method. The available methods are: md5 checksum comparison.
Settings available for each assert:
| Setting | Description | Default |
|---|---|---|
actual |
Path to be added to NFT_OUTPUT to derive output file to be checked by this assertion. |
required |
expect |
Path to expected output file for comparison to actual. |
required |
method |
Comparison method to be used for comparing files. Available: md5 |
md5 |
script |
Custom comparison script that can be run from the command line with 2 positional arguments: actual and then expect. Script must return an exit code of 0 for success and anything else for failure. |
None |
Testing for NFTest itself can be done through pytest by running the following:
pytest
in the root of the repository directory.
- Issue tracker to report errors and enhancement ideas.
- Discussions can take place in tool-NFTest Discussions
- tool-NFTest pull requests are also open for discussion
Please see list of Contributors at GitHub.
Author: Yash Patel, Chenghao Zhu, Helena Winata
NFTest is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
NFTest is a tool for automating Nextflow pipeline testing.
Copyright (C) 2021-2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.