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Third-Party Licenses

This document lists all third-party tools, libraries, and software components used in the EFSA Pipeline, along with their respective licenses and source locations.

The EFSA Pipeline itself is licensed under the European Union Public Licence v1.2 (EUPL-1.2).


License Compatibility Summary

EUPL-1.2 is a copyleft license. Its Appendix explicitly lists compatible licenses for combined/derivative work distribution (GPL-2.0, GPL-3.0, AGPL-3.0, LGPL-2.1, LGPL-3.0, MPL-2.0, EPL-1.0, CeCILL-2.1, and others). Key notes:

Compatibility Class Licenses Status
Permissive (no restrictions) MIT, BSD-2-Clause, BSD-3-Clause, Apache-2.0, Artistic-2.0, PSF-2.0 Compatible
Weak copyleft LGPL-2.1, LGPL-3.0 Compatible (EUPL-1.2 Appendix)
Strong copyleft GPL-2.0, GPL-3.0 Compatible (EUPL-1.2 Appendix)
Database / data licenses Varies by SNPEff database source Verify per database

Important: The pipeline invokes all bioinformatics tools as separate processes inside isolated Docker containers. No tool code is statically or dynamically linked into the pipeline source. This limits copyleft obligations to distribution of the containers themselves, not the pipeline scripts.

Governmental / Commercial Use: All tools listed below use OSI-approved open-source licenses. None impose academic-only or non-commercial restrictions at the license level. However, some tools' databases (e.g., ClinVar, dbSNP used by SNPEff) may carry additional terms — verify before distribution.


1. Bioinformatics Tools (Containerized)

Sequence Alignment & Mapping

Tool Version License Source URL
minimap2 2.30 MIT https://github.com/lh3/minimap2
BWA 0.7.17 GPL-3.0-or-later https://github.com/lh3/bwa
MUMmer (nucmer, delta-filter, show-coords) 4.0.1 Artistic-2.0 https://github.com/mummer4/mummer

Structural Variant Calling

Tool Version License Source URL
CuteSV 2.1.3 MIT https://github.com/tjiangHIT/cuteSV
Sniffles 2.7.3 MIT https://github.com/fritzsedlazeck/Sniffles
DeBreak 1.2 (commit-pinned) MIT https://github.com/Maggi-Chen/DeBreak
DELLY 1.7.3 BSD-3-Clause https://github.com/dellytools/delly
SURVIVOR commit 07404b74 MIT https://github.com/fritzsedlazeck/SURVIVOR
FreeBayes 1.2.0 MIT https://github.com/freebayes/freebayes

Variant Processing & Annotation

Tool Version License Source URL
bcftools 1.23 MIT https://github.com/samtools/bcftools
SAMtools 1.23 MIT https://github.com/samtools/samtools
HTSlib (bgzip, tabix) 1.23 MIT https://github.com/samtools/htslib
Picard 3.4.0 MIT https://github.com/broadinstitute/picard
SnpEff 4.1k LGPL-3.0-only https://github.com/pcingola/SnpEff
Truvari 5.4.0 MIT https://github.com/ACEnglish/truvari

Genome Comparison

Tool Version License Source URL
SyRI 1.7.1 MIT https://github.com/schneebergerlab/syri
gffread 0.12.7 MIT https://github.com/gpertea/gffread

Quality Control

Tool Version License Source URL
FastQC 0.11.9 GPL-3.0-or-later https://github.com/s-andrews/FastQC
MultiQC 1.33 GPL-3.0-or-later https://github.com/MultiQC/MultiQC
NanoPlot 1.46.2 MIT https://github.com/wdecoster/NanoPlot
mosdepth 0.3.12 MIT https://github.com/brentp/mosdepth

Read Processing

Tool Version License Source URL
TrimGalore 0.6.10 GPL-3.0-or-later https://github.com/FelixKrueger/TrimGalore
cutadapt 4.9 MIT https://github.com/marcelm/cutadapt

Compression Utilities

Tool Version License Source URL
pbzip2 1.1.13 BSD-3-Clause http://compression.ca/pbzip2/
pigz system zlib License https://zlib.net/pigz/

2. Python Packages

Runtime Dependencies

Package Version License Source URL
biopython 1.85 BSD-3-Clause AND Biopython License https://biopython.org
numpy 2.2.6 BSD-3-Clause https://numpy.org
pysam 0.23.3 MIT https://github.com/pysam-developers/pysam
structlog 25.4.0 MIT OR Apache-2.0 https://github.com/hynek/structlog
typing_extensions 4.15.0 PSF-2.0 https://github.com/python/typing_extensions

Development / Test Dependencies

Package Version License Source URL
pytest 8.4.2 MIT https://github.com/pytest-dev/pytest

3. Workflow Runtime

Component Version License Source URL
Nextflow 25.10.4 Apache-2.0 https://github.com/nextflow-io/nextflow
nf-schema (plugin) 2.4.2 Apache-2.0 https://github.com/nextflow-io/nf-schema
Docker Engine 29.3.1 Apache-2.0 https://github.com/moby/moby
Alpine Linux 3.23 Mixed (see note) https://alpinelinux.org
OpenJDK 17 (JRE) GPL-2.0 with Classpath Exception https://openjdk.org

Note on Alpine Linux: Alpine itself is MIT-licensed, but it packages third-party software under their respective licenses.


4. Documentation Tools

Component Version License Source URL
MkDocs Material latest MIT https://github.com/squidfunk/mkdocs-material
mkdocs-mermaid2-plugin 10.9.0 MIT https://github.com/fralau/mkdocs-mermaid2-plugin

5. Container Base Images

Image Version / SHA256 Source
staphb/bcftools 1.23@sha256:22f4ddfd... https://github.com/StaPH-B/docker-builds
staphb/samtools 1.23@sha256:ed378537... https://github.com/StaPH-B/docker-builds
staphb/htslib 1.23@sha256:400e7c4e... https://github.com/StaPH-B/docker-builds
staphb/mummer 4.0.1@sha256:f4106644... https://github.com/StaPH-B/docker-builds
staphb/nanoplot 1.46.2@sha256:824dbbe1... https://github.com/StaPH-B/docker-builds
staphb/multiqc 1.33@sha256:4dbb26ba... https://github.com/StaPH-B/docker-builds
biocontainers/bwa v0.7.17_cv1@sha256:9479b73e... https://biocontainers.pro
biocontainers/fastqc v0.11.9_cv8@sha256:82e5fa41... https://biocontainers.pro
biocontainers/freebayes v1.2.0-2-deb_cv1@sha256:1ce0e08e... https://biocontainers.pro
biocontainers/snpeff v4.1k_cv3@sha256:200e8122... https://biocontainers.pro
broadinstitute/picard 3.4.0@sha256:dda3ad26... https://hub.docker.com/r/broadinstitute/picard
dellytools/delly v1.7.3@sha256:045aba10... https://github.com/dellytools/delly
ecomolegmo/cutesv v1.0.4@sha256:9c29e67b... Internal build (based on cuteSV MIT)
ecomolegmo/debreak v1.0.3@sha256:f2d8f9b5... Internal build (based on DeBreak MIT)
ecomolegmo/minimap2 v2.30@sha256:50d38b71... Internal build (based on minimap2 MIT)
ecomolegmo/sniffles v1.0.3@sha256:d3875e4e... Internal build (based on Sniffles MIT)
ecomolegmo/survivor v1.0.3@sha256:90263d6b... Internal build (based on SURVIVOR MIT)
ecomolegmo/syri v1.0.4@sha256:789d5cdf... Internal build (based on SyRI MIT)
ecomolegmo/mosdepth v1.0.1@sha256:802cc917... Internal build (based on Mosdepth GPL-3.0)
ecomolegmo/trimgalore v1.0.1@sha256:802cc917... Internal build (based on TrimGalore GPL-3.0)
ecomolegmo/truvari v1.0.3@sha256:ae346a3b... Internal build (based on Truvari MIT)

License Texts

Full license texts for each component are available at their respective source URLs. The licenses referenced in this document are:

  • MIT — https://opensource.org/licenses/MIT
  • Apache-2.0 — https://www.apache.org/licenses/LICENSE-2.0
  • GPL-3.0 — https://www.gnu.org/licenses/gpl-3.0.html
  • GPL-2.0 — https://www.gnu.org/licenses/gpl-2.0.html
  • LGPL-3.0 — https://www.gnu.org/licenses/lgpl-3.0.html
  • BSD-3-Clause — https://opensource.org/licenses/BSD-3-Clause
  • Artistic-2.0 — https://opensource.org/licenses/Artistic-2.0
  • PSF-2.0 — https://docs.python.org/3/license.html
  • EUPL-1.2 — https://joinup.ec.europa.eu/collection/eupl/eupl-text-eupl-12

Last updated: 2026-03-29 Generated from Nextflow config, Dockerfiles, and requirements.txt in the efsa_pipeline repository.