Find the pipeline you want to start from the CLI by obtaining a list of pipelines associated with your project:
icav2projectpipelineslist
IDCODEDESCRIPTIONfbd6f3c3-cb70-4b35-8f57-372dce2aaf98DRAGENSomatic3.9.5TheDRAGENSomatictoolidentifiessomaticvariantsb4dc6b91-5283-41f6-8095-62a5320ed092 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.
Noofitems: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:
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
Currently, this step for CWL requires the use of the ICA API to access the configuration settings of a project analyses that ran successfully. It is optional for Nextflow since the XML configuration file can be accessed in the ICA GUI.
Nextflow XML file parameters
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
<pd:toolcode="map_align">
and subsequent labels of parameters with a similar structure
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
icav2 projectpipelines start cwl $(pipelineID) --user-reference 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
analysisStorage.description1.2TBanalysisStorage.id6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0analysisStorage.nameSmallanalysisStorage.ownerId8ec463f6-1acb-341b-b321-043c39d8716aanalysisStorage.tenantIdf91bb1a0-c55f-4bce-8014-b2e60c0ec7d3analysisStorage.tenantNameica-cp-adminanalysisStorage.timeCreated2021-11-05T10:28:20ZanalysisStorage.timeModified2021-11-05T10:28:20Zid51abe34a-2506-4ab5-adef-22df621d95d5ownerId47793c21-75a6-3aa8-8147-81b354d0af4dpipeline.analysisStorage.description1.2TBpipeline.analysisStorage.id6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0pipeline.analysisStorage.nameSmallpipeline.analysisStorage.ownerId8ec463f6-1acb-341b-b321-043c39d8716apipeline.analysisStorage.tenantIdf91bb1a0-c55f-4bce-8014-b2e60c0ec7d3pipeline.analysisStorage.tenantNameica-cp-adminpipeline.analysisStorage.timeCreated2021-11-05T10:28:20Zpipeline.analysisStorage.timeModified2021-11-05T10:28:20Zpipeline.codeDRAGENSomatic3.9.5pipeline.description The DRAGEN Somatic tool identifies somatic variants which can exist at low allele frequencies in the tumor sample. The pipeline can analyze tumor/normal pairs and tumor-only sequencing data. The normal sample, if present, is used to avoid calls at sites with germline variants or systematic sequencing artifacts. Unlike germline analysis, the somatic platform makes no ploidy assumptions about the tumor sample, allowing sensitive detection of low-frequency alleles.
pipeline.idfbd6f3c3-cb70-4b35-8f57-372dce2aaf98pipeline.languageCWLpipeline.ownerIde9dd2ff5-c9ba-3293-857e-6546c5503d76pipeline.tenantId55cb0a54-efab-4584-85da-dc6a0197d4c4pipeline.tenantNameilmn-dragenpipeline.timeCreated2021-11-23T22:55:49Zpipeline.timeModified2021-12-09T16:42:14Zreferencekyle-test-somatic-9-DRAGENSomatic3_9_5-bc56d4b1-f90e-4039-b3a4-b11d29263e4estatusREQUESTEDsummarytenantIdb5b750a6-49d4-49de-9f18-75f4f6a81112tenantNameilmn-ccitimeCreated2022-03-16T22:48:31ZtimeModified2022-03-16T22:48:31ZuserReferencekyle-test-somatic-9
Unsuccessful Response Pipeline ID not formatted correctly
400 Bad Request : ICA_API_004 : com.fasterxml.jackson.databind.exc.InvalidFormatException: Cannot deserialize value of type `java.util.UUID` from String "8f57-372dce2aaf98": UUID has to be represented by standard 36-char representation
at [Source: (io.undertow.servlet.spec.ServletInputStreamImpl); line: 1, column: 983] (through reference chain: com.bluebee.rest.v3.publicapi.dto.analysis.SearchMatchingActivationCodesForCwlAnalysisDto["pipelineId"]) (ref. c9cd9090-4ddb-482a-91b5-8471bff0be58)
Check that the pipeline ID is correct based on icav2 projectpipelines list
File ID not found
404 Not Found : ICA_GNRC_001 : Could not find data with ID [fil.35dec404fb37d08d9adf63307] (ref. 91b70c3c-378c-4de2-acc9-794bf18258ec)
Check that the file ID is correct based on icav2 projectdata list
Parameter not found
400 Bad Request : ICA_EXEC_007 : The specified variableName [DRAGEN] does not exist. Make sure to use an existing variableName (ref. ab296d4e-9060-412c-a4c9-562c63450022)
Create Launch Command 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
Response status can be used to determine if the pipeline was submitted successfully
status options: REQUESTED,SUCCEEDED,FAILED,ABORTED
analysisStorage.description1.2TBanalysisStorage.id6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0analysisStorage.nameSmallanalysisStorage.ownerId8ec463f6-1acb-341b-b321-043c39d8716aanalysisStorage.tenantIdf91bb1a0-c55f-4bce-8014-b2e60c0ec7d3analysisStorage.tenantNameica-cp-adminanalysisStorage.timeCreated2021-11-05T10:28:20ZanalysisStorage.timeModified2021-11-05T10:28:20Zid9b8f9e84-2e7f-4adb-92e5-738b032c2328ownerId47793c21-75a6-3aa8-8147-81b354d0af4dpipeline.analysisStorage.description1.2TBpipeline.analysisStorage.id6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0pipeline.analysisStorage.nameSmallpipeline.analysisStorage.ownerId8ec463f6-1acb-341b-b321-043c39d8716apipeline.analysisStorage.tenantIdf91bb1a0-c55f-4bce-8014-b2e60c0ec7d3pipeline.analysisStorage.tenantNameica-cp-adminpipeline.analysisStorage.timeCreated2021-11-05T10:28:20Zpipeline.analysisStorage.timeModified2021-11-05T10:28:20Zpipeline.codeDRAGENSomaticEnrichment3-10-4pipeline.description The DRAGEN Somatic Enrichment pipeline identifies somatic variants which can exist at low allele frequencies in the tumor sample.
pipeline.idb4dc6b91-5283-41f6-8095-62a5320ed092pipeline.languageNEXTFLOWpipeline.ownerIde9dd2ff5-c9ba-3293-857e-6546c5503d76pipeline.tenantId55cb0a54-efab-4584-85da-dc6a0197d4c4pipeline.tenantNameilmn-dragenpipeline.timeCreated2022-03-07T18:09:38Zpipeline.timeModified2022-03-08T17:47:20Zreference somatic-3-10-test5-DRAGEN Somatic Enrichment 3-10-4-3df131a2-2187-489a-b9f8-140e3ec5efb0
statusREQUESTEDtenantIdb5b750a6-49d4-49de-9f18-75f4f6a81112tenantNameilmn-ccitimeCreated2022-07-13T22:44:47ZtimeModified2022-07-13T22:44:47ZuserReferencesomatic-3-10-test5