2.6.0

New Features

• Added --rsfish_background parameter for controlling RS-FISH background subtraction
• Added --rsfish_intensity parameter for controlling RS-FISH intensity calculation
• Updated to RS-FISH-Spark 1.0.2

Bug Fixes

• Fixed tile tokenization for compatibility with Nextflow 24.x

Full Changelog: 2.5.0...2.6.0

2.5.0

New Features

• Added "all" option for stitching_ref
• Made stitching retile step optional
• Added per-channel RS-FISH parameters
• Improved documentation

Bug Fixes

• Removed unnecessary --nv flag to address issues with newer GLIBC systems
• error in intensity_measurements.py by @wangyuhan01 in #14
• git clone needs --recursive as external-modules/spark is a submodule by @orena1 in #23

New Contributors

• @wangyuhan01 made their first contribution in #14
• @orena1 made their first contribution in #23

Full Changelog: 2.4.0...2.5.0

2.4.0

Full Changelog: 2.3.0...2.4.0

2.3.0

• Fixed warp spots when using RS-FISH
• Update default parameters to accommodate large data sets
• Use AWS ECR by default for fetching containers to eliminate throttling errors with DockerHub
• Many documentation improvements

Full Changelog: 2.2.0...2.3.0

2.2.0

• Added support for RS-FISH spot detection
• Fixed pipeline so that flatfield correction is used
• Improved directory naming to reduce conflicts on clusters
• Improved error reporting for Spark jobs

Full Changelog: 2.1.0...2.2.0

Release 2.1.0

Bug fixes and better example data sets, including a "tiny" data set that can be run quickly for regression testing.

Release 2.0.0

Significant refactoring of the parameters to make it easy to run the pipeline on Nextflow Tower.

1. Fixed several issues related to running on AWS
2. Added a download step which downloads a manifest of files, to make it easier to test the demo sets on AWS
3. Greatly simplified directory handling with shared_work_dir
4. Added a publishing step, to copy data onto S3 after the pipeline is complete
5. Added support for CZI file name patterns in the stitching pipeline

Release 1.4.0

Snapshot stable release before merging tower branch for running on Nextflow Tower.

Release 1.1.0

Updated to new version of spot assignment, and made improvements to demo scripts and documentation.

Release 1.0.0

The pipeline is now feature complete and successfully runs end-to-end on medium test data with both local and LSF executors.