tw pipelines

Manage pipelines

Run tw pipelines -h to view the list of supported operations.

Pipelines define pre-configured workflows in a workspace. A pipeline consists of a workflow repository, launch parameters, and a compute environment.

tw pipelines list

List pipelines

tw pipelines list [OPTIONS]

Options

Option	Description	Required	Default
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
-l, --labels	Show labels.	No	false
-f, --filter	Show only pipelines that contain the given word	No
--visibility	Show pipelines: all, private, shared [default: private].	No	private
--page	Page number for paginated results (default: 1)	No
--offset	Row offset for paginated results (default: 0)	No
--max	Maximum number of records to display (default: 100)	No

tw pipelines add

Add a pipeline

tw pipelines add [OPTIONS] <PIPELINE_URL>

Arguments

Argument	Description	Required
PIPELINE_URL	Nextflow pipeline URL	Yes

Options

Option	Description	Required	Default
-n, --name	Pipeline name. Must be unique within the workspace.	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
-d, --description	Pipeline description.	No
--version-name	Initial pipeline version name.	No
--labels	Labels to apply to the resource. Provide comma-separated label values (use key=value format for resource labels). Labels will be created if they don't exist	No
--pipeline-schema-id	Pipeline schema identifier to use.	No
-c, --compute-env	Compute environment identifier where the pipeline will run. Defaults to workspace primary compute environment if omitted. Provide the name or identifier.	No
--work-dir	Work directory path where workflow intermediate files are stored. Defaults to compute environment work directory if omitted.	No
-p, --profile	Array of Nextflow configuration profile names to apply.	No
--params-file	Pipeline parameters in JSON or YAML format. Provide the path to a file containing the content.	No
--revision	Git revision, branch, or tag to use. Use --commit-id to pin to a specific commit within the revision.	No
--commit-id	Specific Git commit hash to pin the pipeline execution to.	No
--config	Nextflow configuration as text (overrides config files). Provide the path to a file containing the content.	No
--pre-run	Add a script that executes in the nf-launch script prior to invoking Nextflow processes. See: https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts. Provide the path to a file containing the content.	No
--post-run	Add a script that executes after all Nextflow processes have completed. See: https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts. Provide the path to a file containing the content.	No
--pull-latest	Pull the latest version of the pipeline from the repository.	No
--stub-run	Execute a stub run for testing (processes return dummy results).	No
--main-script	Alternative main script filename. Default: main.nf.	No
--entry-name	Workflow entry point name when using Nextflow DSL2.	No
--schema-name	Name of the pipeline schema to use.	No
--user-secrets	Array of user secrets to make available to the pipeline.	No
--workspace-secrets	Array of workspace secrets to make available to the pipeline.	No

Run tw pipelines add -h to view the required and optional fields for adding your pipeline.

Add a pre-configured pipeline to the Launchpad:

tw pipelines add --name=my_rnaseq_nf_pipeline \
--params-file=my_rnaseq_nf_pipeline_params.yaml \
--config=<path/to/nextflow/conf/file> \
https://github.com/nextflow-io/rnaseq-nf

New pipeline 'my_rnaseq_nf_pipeline' added at user workspace

The optional --params-file flag is used to pass a set of default parameters that will be associated with the pipeline in the Launchpad.

The optional --config flag is used to pass a custom Nextflow configuration file — configuration values passed here override the same values in the default pipeline repository nextflow.conf file. When this flag is set, all configuration values specified in Platform pipeline or compute environment Nextflow config fields are ignored.

tip

The params-file or --config file must be a YAML or JSON file using Nextflow configuration syntax.

tw pipelines delete

Remove a pipeline

tw pipelines delete [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No

tw pipelines view

View pipeline details

tw pipelines view [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
--version-id	Pipeline version identifier	Yes
--version-name	Pipeline version name	Yes

tw pipelines update

Update a pipeline

tw pipelines update [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
-d, --description	Pipeline description	No
--new-name	Pipeline new name	No
-c, --compute-env	Compute environment identifier where the pipeline will run. Defaults to workspace primary compute environment if omitted. Provide the name or identifier.	No
--work-dir	Work directory path where workflow intermediate files are stored. Defaults to compute environment work directory if omitted.	No
-p, --profile	Array of Nextflow configuration profile names to apply.	No
--params-file	Pipeline parameters in JSON or YAML format. Provide the path to a file containing the content.	No
--revision	Git revision, branch, or tag to use. Use --commit-id to pin to a specific commit within the revision.	No
--commit-id	Specific Git commit hash to pin the pipeline execution to.	No
--config	Nextflow configuration as text (overrides config files). Provide the path to a file containing the content.	No
--pre-run	Add a script that executes in the nf-launch script prior to invoking Nextflow processes. See: https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts. Provide the path to a file containing the content.	No
--post-run	Add a script that executes after all Nextflow processes have completed. See: https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts. Provide the path to a file containing the content.	No
--pull-latest	Pull the latest version of the pipeline from the repository.	No
--stub-run	Execute a stub run for testing (processes return dummy results).	No
--main-script	Alternative main script filename. Default: main.nf.	No
--entry-name	Workflow entry point name when using Nextflow DSL2.	No
--schema-name	Name of the pipeline schema to use.	No
--user-secrets	Array of user secrets to make available to the pipeline.	No
--workspace-secrets	Array of workspace secrets to make available to the pipeline.	No
--pipeline-schema-id	Pipeline schema identifier to use.	No
--pipeline	Nextflow pipeline URL	No
--allow-draft	If versionable fields change, keep the new version as an unnamed draft instead of auto-naming and promoting it to default.	No
--version-id	Pipeline version identifier	Yes
--version-name	Pipeline version name	Yes

The default launch parameters can be changed with the update command:

tw pipelines update --name=my_rnaseq_nf_pipeline \
--params-file=my_rnaseq_nf_pipeline_params_2.yaml

tw pipelines export

Export a pipeline

tw pipelines export [OPTIONS] [FILENAME]

Arguments

Argument	Description	Required
FILENAME	File name to export	No

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
--version-id	Pipeline version identifier	Yes
--version-name	Pipeline version name	Yes

Export a pipeline configuration as JSON for scripting and reproducibility.

Command:

tw pipelines export --name=my_rnaseq_nf_pipeline my_rnaseq_nf_pipeline_v1.json

Example output:

Pipeline exported into 'my_rnaseq_nf_pipeline_v1.json'

tw pipelines import

Add a pipeline from file content

tw pipelines import [OPTIONS] <FILENAME>

Arguments

Argument	Description	Required
FILENAME	File name to import	Yes

Options

Option	Description	Required	Default
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
-c, --compute-env	Compute environment name (defaults to value defined in JSON compute environment file)	No
--overwrite	Overwrite the pipeline if it already exists.	No	false

Import a pipeline into a workspace from a previously exported JSON file.

Command:

tw pipelines import --name=my_rnaseq_nf_pipeline_v1 ./my_rnaseq_nf_pipeline_v1.json

Example output:

New pipeline 'my_rnaseq_nf_pipeline_v1' added at user workspace

tw pipelines labels

Manage pipeline labels

tw pipelines labels [OPTIONS] [labels]

Arguments

Argument	Description	Required
<labels>	Comma-separated list of labels.	No

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
--no-create	Assign labels without creating the ones which were not found.	No
--operations, -o	Type of operation (set, append, delete) [default: set].	No	set

tw pipelines versions

Manage pipeline versions

tw pipelines versions

tw pipelines versions list

List pipeline versions

tw pipelines versions list [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
-f, --filter	Search pipeline versions by name prefix. Also supports keyword filters: versionName, versionId, versionHash. Multiple filters can be combined e.g. 'myPipeline versionName:<name> versionHash:<hash>'.	No
--is-published	Show only published pipeline versions if true, draft versions only if false, all versions by default	No
--full-hash	Show full-length hash values without truncation	No
--page	Page number for paginated results (default: 1)	No
--offset	Row offset for paginated results (default: 0)	No
--max	Maximum number of records to display (default: 100)	No

tw pipelines versions manage

Manage a pipeline version name or default version status

tw pipelines versions manage [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	Yes
-n, --name	Pipeline name	Yes
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
--version-id	Pipeline version identifier	Yes
--version-name	Pipeline version name	Yes
--new-name	New name for the pipeline version	No
--set-default	Set this version as the default	No