Sbpack

- 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

Quick fix to sbpack positional arguments

What's Changed
* Feature/sample sheet support by pavlemarinkovic in https://github.com/rabix/sbpack/pull/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**: https://github.com/rabix/sbpack/compare/2023.11.9rc1...2024.01.04rc1

- `sbcopy` can now be used to copy apps between different environments. By using `--profile` argument, if two profiles are specified, the first will be used as the source (env where the app you want to copy is located) and the second as the target (env where the project you want the app to be copied to is located).
- "--sb-inputs", "--sb-outputs" and "--manual-validation" have been removed
- `--execution-mode` argument with two valid values (single-instance, multi-instance) has been added. This will set the hint on app level which will be taken into consideration when setting up a new draft task using the app.

This version brings with it a few updates:

- Ability to specify executor version though --executor-version for sbpack-nf. This will allow users to specify which executor version they want to use.
- Revision note customization through --revision-note. Users can now add customized revision notes.
- Ability to specify both input and output schema file separately in CWL or (tower.yml specification)[https://help.tower.nf/22.1/reports/overview/#reports-implementation]. This will allow users to use tower yml to define some of the workflow outputs.
- Manual validation option. Users can now initiate manual validation by using --manual-validation in the command line of sbpack-nf. This can make it easier to properly define what types certain ambiguous inputs are, without the need to edit the CWL schema.

Minor fixes