2024.12.17

New Features

Image processing

sbpack_nf can now process markdown and html images, and add them to the app description.

Better manifests

sbmanifest can now process file IDs into vs:// paths

2024.10.30

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.

2024.10.25

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.

2024.08.28rc1

Using wrabbit 0.2.2

2024.07.11rc1

Using wrabbit 0.2.1

2024.06.03rc1

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

2024.05.21rc1

Bugfix: using latest wrabbit version (0.1.2)

2024.05.07rc1

• It is now possible to give apps names instead of it defaulting to the id by using the --app-name argument.
• Using the --exclude argument, it is now possible to provide glob patterns that sbpack will avoid when uploading contents from a code package.
• Addition of sbmanifest - tool that remaps contents of local manifests/sample sheets and uploads it to platform with file paths compatible with the platform file system

2024.02.02rc1

Quick fix to sbpack positional arguments

2024.01.04rc1

What's Changed

• Feature/sample sheet support by @pavlemarinkovic in #79

• Added support for autogenerating sample sheet function(s) for Nextflow app wrapper.
• sbpack will now avoid overwriting previous version of sb_nextflow_schema.yaml
• Enums will be better parsed and generated
• New --auto mode tries to locate as many files and inputs for generating the app automatically
• The logic for uploading the app code package and the app itself has been updated. It now first tires to create the app wrapper, and if it succeeds then tries to upload the code package.

Full Changelog: 2023.11.9rc1...2024.01.04rc1