fovus pipeline create

fovus pipeline create

Create pipeline.

Local workflow host creates a pipeline record only. You run Nextflow on your workstation; PIPELINE_DIRECTORY is optional and is not used.

Remote workflow host creates the pipeline and starts execution on Fovus-hosted compute (configuration required). Provide PIPELINE_DIRECTORY as your local Nextflow project folder; the folder is created if it does not exist yet. Files are uploaded to remote storage and the pipeline id is saved for that directory after a successful create. If a pipeline id is already stored for the directory, you must confirm before it is replaced unless you pass –override or run with –silence (non-interactive), which replaces it by default.

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

Usage

fovus pipeline create [OPTIONS] [PIPELINE_DIRECTORY]

Options

--pipeline-directory <legacy_pipeline_directory>

Deprecated: use the PIPELINE_DIRECTORY positional argument instead.

-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 | custom

--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.

--override

Replace the existing pipeline id for the pipeline directory without prompting (remote workflow host only).

Arguments

PIPELINE_DIRECTORY

Optional argument