fovus pipeline create¶

Create pipeline.

For local workflow host: creates a pipeline record; you run Nextflow manually on your workstation.

For remote workflow host: creates and starts pipeline execution on EC2 (requires configuration). When PIPELINE_DIRECTORY is provided for remote, uploads files to pipelines/<pipeline-id> (similar to job create).

PIPELINE_DIRECTORY is the local Nextflow project dir (default: current directory). Used for upload when workflow host is remote.

Use -c/–config to pass a pipeline config JSON. CLI options override config values.

Usage

fovus pipeline create [OPTIONS]

Options

--pipeline-directory <pipeline_directory>¶: Local directory to upload to remote pipeline storage. If omitted, no files are uploaded.

-c, --config <config_path>¶: Path to pipeline config JSON. Can specify workflowHost and all create arguments; CLI options override config.

--workflow-host <workflow_host>¶

Where the workflow runs: local (on your workstation) or remote (on Fovus-hosted compute). Default: remote, or from config workflowHost if -c is used.

Options:: local | remote

--workflow-manager <workflow_manager>¶

Workflow engine. Only Nextflow is supported (maps to configuration.workflowManager NEXTFLOW).

Options:: nextflow

--name <name>¶: The pipeline name. Overrides config if provided.

--project-name <project_name>¶: The project name associated with your pipeline. If omitted, the default project will be used. Use ‘None’ to specify no project.

--auto-delete-days <auto_delete_days>¶: Number of days after which the pipeline will be permanently deleted. Only applicable when workflow host is remote.

--setup-command <setup_command>¶: Setup command for remote execution (e.g. git clone). Overrides config if provided.

--run-command <run_command>¶: Run command for remote execution (e.g. nextflow run nf-core/rnaseq). Overrides config if provided.

--include-paths <include_paths>¶: Include only these paths when uploading pipeline directory (remote workflow host). Relative paths inside PIPELINE_DIRECTORY. Use * and ? for wildcards. Only one of –include-paths or –exclude-paths.

--exclude-paths <exclude_paths>¶: Exclude these paths when uploading pipeline directory (remote workflow host). Relative paths inside PIPELINE_DIRECTORY. Use * and ? for wildcards. Only one of –include-paths or –exclude-paths.