tw pipelines

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

Pipelines define pre-configured workflows in a workspace. A saved pipeline includes the repository source, launch parameters, compute environment, and, in newer Platform releases, optional persisted schemas and multiple saved versions.

Pipeline versioning

Seqera Platform CLI 0.24 adds support for pipeline versioning workflows:

• create a saved pipeline with an initial version name
• list saved versions for a pipeline
• target a specific version by --version-id or --version-name
• promote a version to default
• update a versionable field and let Platform create a new version

tw pipelines list

List pipelines.

tw pipelines list [OPTIONS]

Options

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

Example

tw pipelines list -w 123456789012345

Example output:

  Pipelines at [my-organization-updated / my-workspace] workspace:


ID              | Name                 | Repository                           | Visibility
    -----------------+----------------------+--------------------------------------+------------
     777888999000111 | rnaseq4              | https://github.com/nf-core/rnaseq    | SHARED
     888999000111222 | nf-core-rnaseq       | https://github.com/nf-core/rnaseq    | SHARED
     999000111222333 | rnaseq2              | https://github.com/nf-core/rnaseq    | SHARED
     555666777888999 | nextflow-hello-saved | https://github.com/nextflow-io/hello | SHARED
     000111222333444 | rnaseqapitest        | https://github.com/nf-core/rnaseq    | SHARED
     111222333444555 | rnaseq3              | https://github.com/nf-core/rnaseq    | SHARED

tw pipelines add

Add a pipeline.

tw pipelines add [OPTIONS] <repository-url>

Options

Option	Description	Required	Default
-n, --name	Pipeline name. Must be unique within the workspace.	Yes	null
<repository-url>	Pipeline repository URL. Must be a full Git repository URL.	Yes	null
-d, --description	Pipeline description.	No	null
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No	TOWER_WORKSPACE_ID
--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 do not exist.	No	null
--version-name	Initial pipeline version name.	No	null
--pipeline-schema-id	Pipeline schema identifier to attach to the saved pipeline.	No	null
-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	null
--work-dir	Work directory path where workflow intermediate files are stored. Defaults to compute environment work directory if omitted.	No	null
-p, --profile	Array of Nextflow configuration profile names to apply.	No	null
--params-file	Pipeline parameters in JSON or YAML format. Provide the path to a file containing the content.	No	null
--revision	Git revision, branch, or tag to use. Use --commit-id to pin a specific commit within that revision.	No	null
--commit-id	Specific Git commit hash to pin the saved pipeline to.	No	null
--config	Nextflow configuration as text (overrides config files). Provide the path to a file containing the content.	No	null
--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	null
--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	null
--pull-latest	Pull the latest version of the pipeline from the repository.	No	null
--stub-run	Execute a stub run for testing (processes return dummy results).	No	null
--main-script	Alternative main script filename. Default: main.nf.	No	null
--entry-name	Workflow entry point name when using Nextflow DSL2.	No	null
--schema-name	Name of the pipeline schema to use.	No	null
--user-secrets	Array of user secrets to make available to the pipeline.	No	null
--workspace-secrets	Array of workspace secrets to make available to the pipeline.	No	null

Example

tw pipelines add \
  --name my-rnaseq \
  --version-name v1.0 \
  --pipeline-schema-id 98765 \
  --revision main \
  --commit-id a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2 \
  --params-file my-rnaseq-params.yaml \
  -w 123456789012345 \
  https://github.com/nextflow-io/rnaseq-nf

Example output:

New pipeline 'my-rnaseq' added at [my-organization / my-workspace] workspace

Use --pipeline-schema-id with a schema uploaded by tw pipeline-schemas add to make that schema part of the saved pipeline definition in Platform.

tw pipelines view

View pipeline details.

tw pipelines view [OPTIONS]

Options

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

If no version is specified, view shows the default saved version.

Example

tw pipelines view -n my-rnaseq --version-name v1.0 -w 123456789012345

The output includes version metadata such as the version name, whether it is the default version, and the version hash, followed by the resolved launch configuration.

tw pipelines update

Update a pipeline.

tw pipelines update [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	No	null
-n, --name	Pipeline name	No	null
--version-id	Pipeline version identifier to update. If omitted, the default saved version is updated.	No	null
--version-name	Pipeline version name to update. If omitted, the default saved version is updated.	No	null
-d, --description	Pipeline description	No	null
--new-name	Pipeline new name	No	null
--pipeline	Nextflow pipeline URL	No	null
--allow-draft	If versionable fields change, keep the new version as an unnamed draft instead of auto-naming and promoting it to default.	No	false
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No	TOWER_WORKSPACE_ID
--pipeline-schema-id	Pipeline schema identifier to attach to the saved pipeline.	No	null
-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	null
--work-dir	Work directory path where workflow intermediate files are stored. Defaults to compute environment work directory if omitted.	No	null
-p, --profile	Array of Nextflow configuration profile names to apply.	No	null
--params-file	Pipeline parameters in JSON or YAML format. Provide the path to a file containing the content.	No	null
--revision	Git revision, branch, or tag to use. Use --commit-id to pin a specific commit within that revision.	No	null
--commit-id	Specific Git commit hash to pin the saved pipeline to.	No	null
--config	Nextflow configuration as text (overrides config files). Provide the path to a file containing the content.	No	null
--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	null
--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	null
--pull-latest	Pull the latest version of the pipeline from the repository.	No	null
--stub-run	Execute a stub run for testing (processes return dummy results).	No	null
--main-script	Alternative main script filename. Default: main.nf.	No	null
--entry-name	Workflow entry point name when using Nextflow DSL2.	No	null
--schema-name	Name of the pipeline schema to use.	No	null
--user-secrets	Array of user secrets to make available to the pipeline.	No	null
--workspace-secrets	Array of workspace secrets to make available to the pipeline.	No	null

Version-aware update behavior:

• Non-versioned changes are applied in place.
• Changing versioned launch fields such as repository revision can cause Platform to create a new saved version.
• By default, the CLI auto-names that new version and promotes it to the default Launchpad version.
• With --allow-draft, the CLI leaves the new version as a draft so you can manage it later with tw pipelines versions.

Example

tw pipelines update \
  --name my-rnaseq \
  --version-name v1.0 \
  --revision release-branch \
  --allow-draft

Example output:

Pipeline 'my-rnaseq' updated at [my-organization / my-workspace] workspace
New draft version 'draft789' created. Use 'tw pipelines versions' to manage it.

tw pipelines versions list

List saved pipeline versions.

tw pipelines versions list [OPTIONS]

Options

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

Example

tw pipelines versions list \
  -n my-rnaseq \
  --is-published true \
  --full-hash

This command shows each version's ID, name, default status, hash, creator, and creation time.

tw pipelines versions manage

Manage a pipeline version name or default status.

tw pipelines versions manage [OPTIONS]

Options

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

Provide at least one of --new-name or --set-default.

Example

tw pipelines versions manage \
  -n my-rnaseq \
  --version-id 7TnlaOKANkiDIdDqOO2kCs \
  --set-default \
  --new-name v2.0

Example output:

Pipeline version '7TnlaOKANkiDIdDqOO2kCs' of pipeline 'my-rnaseq' updated at workspace [my-organization / my-workspace]

tw pipelines delete

Remove a pipeline.

tw pipelines delete [OPTIONS]

Options

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

Example

tw pipelines delete -n my-rnaseq -w 123456789012345

tw pipelines export

Export a pipeline.

tw pipelines export [OPTIONS] [FILENAME]

Options

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

If you do not provide a version selector, export uses the default saved version.

Example

tw pipelines export -n my-rnaseq --version-name v2.0 my-rnaseq-export.json

tw pipelines import

Add a pipeline from file content.

tw pipelines import [OPTIONS]

Options

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

Example

tw pipelines import -n my-rnaseq-imported -w 123456789012345 my-rnaseq-export.json

tw pipelines labels

Manage pipeline labels.

tw pipelines labels [OPTIONS]

Options

Option	Description	Required	Default
-i, --id	Pipeline identifier	No	null
-n, --name	Pipeline name	No	null
--no-create	Assign labels without creating the ones that were not found.	No	null
--operations, -o	Type of operation (set, append, delete) [default: set].	No	set

Example

tw pipelines labels -n my-rnaseq -w 123456789012345 project=demo

tip

The --params-file flag is used to pass default launch parameters that are associated with the saved pipeline in the Launchpad.

tip

The --config file must use Nextflow configuration syntax.