nft-utils

nf-test plugin with utility functions for pipeline-level snapshot testing.

Features

• sanitizeOutput() - clean process outputs for stable snapshots
• filterNextflowOutput() - remove variable content from stdout/stderr
• getAllFilesFromPath() - list files from local or S3 paths
• removeNextflowVersion() - strip Nextflow version from YAML files
• nfcoreInstall() - install nf-core modules for testing
• curlAndExtract() - download and extract archives in test setup

Full documentation at nf-co.re/nft-utils.

Development

Requires Nextflow, nf-test, and Maven.

# Install conda environment
mamba env create -f environment.yml
mamba activate env_nft_utils

# Compile the package
mvn -B clean verify

# Run all tests
nf-test test --plugins target/nft-utils-*.jar --verbose --debug tests/

# Run a single test and update snapshots
nf-test test --plugins target/nft-utils-*.jar --update-snapshot tests/sanitizeOutput/

# Test with no plugins installed
nf-test test --plugins target/nft-utils-*.jar --config tests_noplugins/nf-test_noplugins.config tests_noplugins/sanitizeOutput/

Credits

nft-utils was created by the nf-core community.

• Adam Talbot
• Edmund Miller
• Igor Trujnara
• James A. Fellows Yates
• Jim Downie
• Jonathan Manning
• Joon Klaps
• Louis Le Nezet
• Lukas Forer
• Matthias Zepper
• Matthieu Muffato
• Maxime U. Garcia
• Nicolas Vannieuwkerke
• Sateesh Peri
• Thiseas C. Lamnidis