Illumina Connected Software

Launch DRAGEN Pipelines on CLI

Prerequisite - Launch a CWL or Nextflow pipeline to completion using the ICA CLI with the intended set of parameters.

Configure CLI and Identify Pipeline ID

Configure and Authenticate ICA command line interface (CLI).

Obtain a list of your projects with their associated IDs:

icav2 projects list
ID                                      NAME         OWNER
a5690b16-a739-4bd7-a62a-dc4dc5c5de6c    Project1     670fd8ea-2ddb-377d-bd8b-587e7781f2b5
ccb0667b-5949-489a-8902-692ef2f31827    Project2     f1aa8430-7058-4f6c-a726-b75ddf6252eb
No of items :  2

Use the ID of the project from the previous step to enter the project context:

icav2 projects enter a5690b16-a739-4bd7-a62a-dc4dc5c5de6c

Find the pipeline you want to start from the CLI by obtaining a list of pipelines associated with your project:

icav2 projectpipelines list
ID                                      CODE					DESCRIPTION      
fbd6f3c3-cb70-4b35-8f57-372dce2aaf98    DRAGEN Somatic 3.9.5			The DRAGEN Somatic tool identifies somatic variants
b4dc6b91-5283-41f6-8095-62a5320ed092    DRAGEN Somatic Enrichment 3-10-4	The DRAGEN Somatic Enrichment pipeline identifies somatic variants which can exist at low allele frequencies in the tumor sample.
No of items :  2

Find the ID associated with your pipeline of interest.

Identify Input File Parameters

To find the input files parameter, you can use a previously launched projectanalyses with the input command.

Find the previous analyses launched along with their associated IDs:

List the analyses inputs by using the ID found in the previous step:

This will return the Input File Codes, as well as the file names and data IDs of the associated data used to previously launch the pipeline

Identify Configuration Settings

You need to use the ICA API to access the configuration settings of a project analyses that ran successfully.

API-based Configuration Settings

  • Generate JWT Token from API Key or Basic login credentials

  • Instructions on how to get an API Key https://illumina.gitbook.io/ica/account-management/am-iam#api-keys

  • If your user has access to multiple domains, you will need to need to add a "?tenant=($domain)" to the request

  • Response to this request will provide a JWT token {"token":($token)}, use the value of the token in further requests

  • Using the API endpoint /api/projects/{projectID}/analyses/{analysisId}/configurations to find the configuration file listing out all of required and optional parameters

The response JSON to this API will have configuration items listed as

Nextflow XML file parameters via GUI (Prior to DRAGEN 4.3)

Click the previous GUI run, and select the pipeline that was run. On the pipeline page, select the XML Configuration Tab to view the configuration settings.

In the "steps" section of the XML file, you will find various steps labeled with

and subsequent labels of parameters with a similar structure

The code should be used to generate the later command line parameters e.g.

--parameters enable_map_align:true

Create Launch Command

CWL

Structure of the final command

icav2 projectpipelines start cwl $(pipelineID) --user-referenc Plus input options

  • Input Options - For CLI, the entire input can be broken down as individual command line arguments

To launch the same analysis as using the GUI, use the same file ID and parameters, if using new data you can use the CLI command icav2 projectdata list to find new file IDs to launch a new instance of the pipeline Required information in Input - Input Data and Parameters

Command Line Arguments

  • This option requires the use of --type input STRUCTURED along with --input and --parameters

  • The input parameter names such as Reference and Tumor_FASTQ_Files in the example below are from the pipeline definition where you can give the parameters a name. You can see which of these were used when the pipeline originally ran, in the Identify Input File Parameters section above. You can also look at the pipeline definitions for the input parameters, for example the code value of these XML inputs.

Successful Response

Unsuccessful: Pipeline ID not formatted correctly

  • Check that the pipeline ID is correct based on icav2 projectpipelines list

Unsuccessful: File ID not found

  • Check that the file ID is correct based on icav2 projectdata list

Unsuccessful: Parameter not found

Nextflow

When using nextflow to start runs, the input-type parameter is not used, but the --project-id is required

Structure of the file command icav2 projectpipelines start nextflow $(pipelineID) --user-reference Plus input options

The Response status can be used to determine if the pipeline was submitted successfully.

PreviousAPI Beginner GuideNextMount projectdata using CLI

Last updated

Was this helpful?