Changelog
=========

Version 1.5-dev
---------------

Core CLI
~~~~~~~~
* Refactored RAFT from a monolithic CLI into a package with focused modules for CLI parsing, dispatch, project setup, module loading, OTS execution, workflow execution, and UI support.
* Added the unified ``raft run`` flow so RAFT can either run an existing project or create-and-run an OTS workflow when the project does not yet exist.
* Added ``update-parameters`` for updating project parameters from generated or external config files.
* Added ``--profile`` support and improved default-profile detection for Nextflow runs.
* Added automatic Singularity fallback behavior when no default Nextflow profile is configured.
* Added runtime bootstrap checks for Java, Nextflow, and Singularity/Apptainer dependencies.
* Added caching of dependency checks in ``.raft.cfg`` to reduce startup overhead.
* Added adaptive Git throttling with jitter and backoff for module and repository access.
* Improved path normalization and ``auto.raft`` command logging behavior.
* Improved parameter extraction and population for generated ``main.nf`` files, including handling for ternary expressions, module-scope assignments, and workflow-generated parameter updates.
* Added ``--include-all-samples`` support to force ``include_all_samples`` parameters in generated projects before execution.
* Expanded manifest validation, FASTQ autocomplete behavior, and HLA allele checking in ``check-manifest``.

UI tools
~~~~~~~~
* Added browser-based manifest and configuration generators for OTS workflows.
* Added the browser-based LENS viewer, including hosted and standalone demo modes.
* Added headless UI support with copy/paste transfer flows for remote or SSH-based usage.
* Added ``generate-reports --demo`` for exploring the LENS viewer without running a workflow.
* Added support for multi-group and timepoint-aware LENS report exploration, joint group comparisons, richer QC summaries, and external annotations.

Datasets
~~~~~~~~
* Added off-the-shelf dataset support through ``--dataset`` in the OTS run path.
* Added dataset-prep cloning, public metadata preparation, and dataset FASTQ staging for OTS projects.
* Improved ENA/EBI FASTQ downloading, including long-accession path handling and clearer progress output.
* Added compatibility for updated GitLab layouts, including legacy and newer repository roots, ``workflows`` and ``subworkflows``, and dataset subgroup fallback behavior.

Cloud
~~~~~
* Added cloud launcher support, cloud input synchronization, GCP uploads, and bundled-transfer support for cloud execution.

Testing
~~~~~~~
* Added broader automated test coverage for the control plane, OTS helpers, workflow execution, API endpoints, QC parsers, and parameter parsing.

Documentation
~~~~~~~~~~~~~
* Added and expanded Sphinx documentation for local usage, cloud usage, datasets, UI flows, and quick-start guidance.


Version 1.4.3
-------------
* Quick documentation and release update for the 1.4 maintenance line.


Version 1.4.2
-------------
* Updated documentation for the 1.4 maintenance line.
* Published the RAFT v1.4.2 maintenance release update.