Changelog

Version 1.5-dev

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.

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.

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.

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

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

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