Releases: usadellab/Trimmomatic
v0.40
This release introduces several new features focused on usability and performance, as well as a complete modernization of the build and testing process.
New Features
-
Advanced Compression Control: Users can now fine-tune the output compression.
- Added parallel compression for GZip and BZip2.
- Added
-compressBlock(default) and-compressStreamoptions to control the compression mode. - Added
-compressLeveloption to specify the compression level for GZip and BZip2 (from 1=fastest to 9=best).
-
Automatic Adapter File Discovery: The
ILLUMINACLIPstep is now more user-friendly. If a full path to the adapter FASTA file is not provided, Trimmomatic will automatically search for the file in the following order:- The
adapterssubdirectory located next to the Trimmomatic.jarfile. - The current working directory.
This removes the need to hard-code paths for the standard adapter files included with the distribution.
- The
-
Poly-G Detection: Added Poly-G adapter sequences to target and remove G-tail artifacts, which are common in Illumina NextSeq and NovaSeq two-color chemistry data.
Build and CI/CD Improvements
-
Maven Integration: The project has been completely migrated to a Maven build system. This standardizes the build process, makes dependency management automatic, and simplifies compiling the project from source.
-
Added GitHub Actions workflows to automate key development processes:
- Automated Testing: Unit tests (JUnit) are now automatically run on every push to ensure code quality and stability.
- Automated Docker Builds: A Docker container is automatically built and published with each new release, simplifying deployment for users.
Docker Support
With each release, a Docker container is automatically built and published to the GitHub Container Registry. You can pull the image for this release using the following command:
docker pull ghcr.io/usadellab/trimmomatic:v0.40v0.39
README