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 project-status for manifest-aware project summaries, workflow-specific status checks, and guided next actions.

  • 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.

  • Added versioned MOTD support and improved startup guidance for missing profiles and runtime dependencies.

  • Added available-workflow-profiles for listing version-specific OTS workflow profiles with descriptions, plus download-refs for pre-populating shared OTS references without creating a project.

  • Improved path normalization and auto.raft command logging behavior.

  • Added --skip-module-fetches to stop OTS setup after staging inputs and scaffolding but before module loading, and disabled argparse abbreviations to avoid ambiguous CLI parsing.

  • 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.

  • Added sample-multiplier-based resource scaling support and the raft_scaling execution profile.

  • Fixed raft_scaling to read sample_multipliers.csv through Nextflow’s file(...) helper and added pre-launch multiplier generation from local or bucket-backed FASTQ sizes so first-run cloud launches can scale resources immediately.

  • Improved missing-dependency guidance with OS-specific installation hints across more Linux distributions.

  • 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.

  • Added portable report bundle generation, byte/progress reporting, PDF/QC bundling, and a generic hosted report viewer path that is no longer LENS-only.

  • Added workflow-owned report UI templates, workflow-configurable report sections, and workflow metadata loading from config repositories.

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.

  • Added project/reference/shared bucket routing, cloud staging progress displays, and manifest-aware FASTQ/reference staging improvements.

  • Added provider-aware default resourceLabels for bucket-backed runs, with s3:// inferring AWS labels and gs:// inferring GCP labels, plus workspace and per-run overrides.

  • Added bucket-auth preflight checks, stricter --resource-label KEY=VALUE validation, improved missing-bucket messaging, and fixes for --fastqs-bucket staging in bucket-backed runs.

  • Added support for synchronizing selected workflow outputs back to local environments after bucket-backed runs.

  • Added locking for shared OTS reference setup so concurrent projects wait instead of corrupting shared downloads or extractions.

  • Improved bucket-backed reference staging with direct cloud-to-cloud GCS copies and clearer failures when required shared references have not been pre-staged.

Workflow execution

  • Added headless-by-default run-demo behavior for browser-based flows, along with improved CLI/UI sequencing during setup.

  • Replaced --keep-intermediates with --delete-intermediates, defaulted generated projects to leave params.clean_intermediates disabled, and made reruns explicitly enable or disable intermediate cleanup.

  • Improved raft run safeguards for existing projects and regenerated incomplete sample_multipliers.csv files from manifest rows and local or remote FASTQ sizes before launch.

  • Improved report discovery, preload behavior, and workflow-specific report handling for generate-reports.

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.

  • Expanded installation, hybrid/cloud, FAQ, troubleshooting, and options docs to cover resource labels, --fastqs-bucket, download-refs, raft_scaling, and intermediate-cleaning behavior.

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.