sbpack_nf command reference
Here is a list describing all available arguments of the sbpack_nf command that is used to convert and push Nextflow apps for execution on the Seven Bridges Platform.
| Argument | Required | Description |
|---|---|---|
-h, --help | Shows the list of all arguments and their corresponding explanations. | |
--profile PROFILE | Optional | SB platform profile as set in the SB API credentials file. If not provided, the default profile will be used. |
--appid APPID | Optional | Provide the destination ID of the Nextflow app once it is pushed to the Seven Bridges Platform. Takes the form {user or division}/{project}/{app_id}. If you are using Enterprise, the {user or division} part is name of your Division on the Platform; otherwise, specify your Platform username. The {project} part is the project to which you want to push the app and {app_id} is the ID you want to assign to the app, for example my-division/my-new-project/my-nextflow-app. This argument is required if pushing to the platform, but not required if generating the sb_nextflow_schema.yaml file locally. |
--workflow-path WORKFLOW_PATH | Required | Path to the main workflow directory (the local directory where the app's files are located). |
--entrypoint ENTRYPOINT | Optional | Relative path to the the main Nextflow file that contains the app's Nextflow code from the workflow directory defined in --workflow-path. If not provided, 'main.nf' will be used if it exists in the workflow directory. If 'main.nf' file does not exist, but only a single '.nf' file is located in the workflow directory, that file will be used. If more than one '.nf' file is detected, an error is raised. |
--sb-package-id SB_PACKAGE_ID | Optional | ID of an already uploaded package. If you have already converted and pushed the app to the Platform, it has its own code package ID, as shown in the code_package key in the sb_nextflow_schema.yaml file. When the package ID is provided, the conversion script will skip the upload step and thus take less time to execute. |
--sb-doc SB_DOC | Optional | Path to the app description document written in Markdown. The document is meant to provide additional details about the app and will be shown when viewing app details on the Platform. If not provided, README.md will be used if available in the same directory where entrypoint file is located. |
--sb-schema SB_SCHEMA | Optional | Path to an existing sb_nextflow_schema file in JSON or YAML format. This allows you to use an existing configuration file where you have already made optimizations (configuration of inputs, outputs, requirements, etc.) for the execution of your app on the Seven Bridges Platform. |
--dump-sb-app | Optional | Dumps the converted app to a local file without pushing it to the Platform. Using this option will enable you to convert the app and generate the sb_nextflow_schema.yaml file to make configuration optimizations prior to pushing the app the Platform. |
--revision-note REVISION_NOTE | Optional | Short description of the changes made when uploading the app to the Seven Bridges Platform. This information will be visible in the app's revision (version) . |
--app-name | Optional | Display name of the application on the Seven Bridges Platform. |
--exclude EXCLUDE [EXCLUDE...] | Optional | Glob patterns of files in the --workflow-path you want to exclude from the code package when it's uploaded to the platform. By default the following patterns are excluded: ['*.git', '*.git*', '.git', '.git*', 'work', '.nextflow.log', '.DS_Store', '.devcontainer', '.editorconfig', '.gitattributes', '.nextflow', '.pre-commit-config.yaml', '.prettierignore', '.prettierrc.yml', '.idea', '.pytest_cache', '*.egg-info'] |
--json | Optional | Creates the sb_nextflow_schema file in JSON format instead of the default YAML. |
Updated about 2 months ago