Sbpack

New Features

Git Repository Support

**1. `--git-url` and `--branch` Parameters Added:**
- `--git-url`: Allows you to specify the URL of a Git repository, enabling direct import of apps from a Git source to the platform.
- `--branch`: When used with `--git-url`, this parameter specifies the branch to clone, giving precise control over which branch is imported.

Enhanced Application Import Workflow

With these new parameters, `sbpack_nf` now supports cloning Git repositories for a more streamlined app import process. This enhancement expands flexibility and improves usability for Git-based workflows, simplifying the migration of applications from Git to the platform.

New tool: sbmanifest
Allows mapping and uploading of local manifests or sample sheets to align file paths with platform requirements.

sbcopy
`sbcopy` now supports app transfers across different environments using --profile. Designate source and target environments for seamless app migration.

sbpack_nf
wrabbit Integration
A new library (wrabbit) has been created to handle CWL wrapper creation and management for `sbpack_nf`. The `sbpack_nf` tool now handles the API and uses wrabbit to create a wrapper for Nextflow tools.

App and Workflow Management
Custom App Naming: Specify custom app names using the --app-name argument.
Exclusion Patterns: Exclude specific files or directories using the --exclude argument, accepting glob patterns for flexible exclusions.
Customizable Revision Notes: Users can now add notes with --revision-note for version clarity.

Execution and Task Setup
Execution Modes: Introduced --execution-mode argument with single-instance and multi-instance options, allowing selection of the execution mode for SevenBridges powered platforms.

Quality of Life Improvements
New Auto Mode
`--auto` mode automatically identifies files and inputs needed for app generation, expediting setup.

File Overwrite Prevention
`sbpack` now prevents overwriting of previous versions for key files like sb_nextflow_schema.yaml.

- Using latest wrabbit version (0.1.3)
- Generating a new nextflow_schema.json, only if none exist