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Pipelines

A Pipeline is a series of Tools with connected inputs and outputs configured to execute in a specific order.

Pipeline Status

Pipelines can only be edited when they are in "Draft" or "Release Candidate" status. Pipeline can only be moved to "Released" Status, when all the Tools in the pipeline are ALSO in "Released" status.
Status
Description
Draft
Fully editable draft.
Release Candidate
The pipeline is ready for release. Editing is locked but the pipeline can be cloned (top right in the details view) to create a new version.
Released
The pipeline is released. A pipeline cannot be released if it contains unreleased tools. Editing is locked but the pipeline can be cloned (top right in the details view) to create a new version.

Create a Pipeline

Pipelines are created and stored within projects.
  1. 1.
    Select a project.
  2. 2.
    From the project menu, select Flow > Pipelines.
  3. 3.
    Select CWL or Nextflow to create a new Pipeline.
  4. 4.
    Configure pipeline settings in the pipeline properties tabs.
  5. 5.
    When creating a graphical CWL pipeline, drag connectors to link tools to input and output files in the canvas. Required tool inputs are indicated by a yellow connector.
  6. 6.
    Select Save.
❗️ Pipelines use the latest tool definition when the pipeline was last saved. Tool changes do not automatically propagate to the pipeline. In order to update the pipeline with the latest tool changes, edit the pipeline definition by removing the tool and re-adding it back to the pipeline.

Pipeline Properties

The following sections describe the tool properties that can be configured in each tab of the pipeline editor.

Graphical vs Code definition

Depending on how you design the pipeline, the displayed tabs differ between the graphical and code definitions. For CWL you have a choice on how to define the pipeline, Nextflow is always defined in code mode.
Language
Graphical (CWL)
Code (CWL)
Code (Nextflow)
Information
x
x
x
Documentation
x
x
x
Definition
x
​
​
XML Configuration
​
x
x
Analysis Report
x
​
​
Metadata Model
x
x
x
workflow.cwl
​
x
​
nextflow.config
​
​
x
main.nf
​
​
x
New File
​
x
x
See the following pages for language-specific details for defining pipelines:

Information

The Information tab provides options for configuring basic information about the pipeline. (small differences exist between the Nextflow and CWL versions)
Field
Entry
Code
The name of the pipeline.
Categories
One or more tags to categorize the pipeline. Select from existing tags or type a new tag name in the field.
Description
A short description of the pipeline.
Proprietary
Hide the pipeline scripts and details from users who do not belong to the tenant who owns the pipeline. This also prevents cloning the pipeline.
Status
The release status of the pipeline.
Storage size
User selectable storage size for running the pipeline. This must be large enough to run the pipeline, but setting it too large incurs unnecessary costs.
Family
A group of pipeline versions. To specify a family, select Change, and then select a pipeline or pipeline family. To change the order of the pipeline, select Up or Down. The first pipeline listed is the default and the remainder of the pipelines are listed as Other versions. The current pipeline appears in the list as this pipeline.
Version comment
A description of changes in the updated version.
Links
External reference links.
The following information becomes visible when viewing the pipeline.
Field
Entry
ID
Unique Identifier of the pipeline.
URN
Identification of the pipeline in Uniform Resource Name
Nextflow Version
User selectable Nextflow version available only for Nextflow pipelines
In addition, the clone function will be shown (top-right). When cloning a pipeline, you become the owner of the cloned pipeline.

Documentation

The Documentation tab provides options for configuring the HTML description for the tool. The description appears in the tool repository but is excluded from exported CWL definitions. If no documentation has been provided, this tab will be empty.

Definition (Graphical)

When using graphical mode for the pipeline definition, the Definition tab provides options for configuring the pipeline using a visualization panel and a list of component menus.
Menu
Description
Machine profiles
Compute types available to use with Tools in the pipeline.
Shared settings
Settings for pipelines used in more than one tool.
Reference files
Descriptions of reference files used in the pipeline.
Input files
Descriptions of input files used in the pipeline.
Output files
Descriptions of output files used in the pipeline.
Tool
Details about the tool selected in the visualization panel.
Tool repository
A list of tools available to be used in the pipeline.
❗️ In graphical mode, you can drag and drop inputs into the visualization panel to connect them to the tools. Make sure to connect the input icons to the tool before editing the input details in the component menu. Required tool inputs are indicated by a yellow connector.

XML Configuration (code)

This page is used to specify all relevant information about the pipeline parameters.

Analysis Report (Graphical)

The Analysis Report tab provides options for configuring pipeline execution reports. The report is composed of widgets added to the tab.

Configure Pipeline Analysis Report (Graphical CWL Only)

The pipeline analysis report appears in the pipeline execution results. The report is configured from widgets added to the Analysis Report tab in the pipeline editor.
  1. 1.
    [Optional] Import widgets from another pipeline.
    1. 1.
      Select Import from other pipeline.
    2. 2.
      Select the pipeline that contains the report you want to copy.
    3. 3.
      Select an import option: Replace current report or Append to current report.
    4. 4.
      Select Import.
  2. 2.
    From the Analysis Report tab, select Add widget, and then select a widget type.
  3. 3.
    Configure widget details.
    Widget
    Settings
    Title
    Add and format title text.
    Analysis details
    Add heading text and select the analysis metadata details to display.
    Free text
    Add formatted free text. The widget includes options for placeholder variables that display the corresponding project values.
    Inline viewer
    Add options to view the content of an analysis output file.
    Analysis comments
    Add comments that can be edited after an analysis has been performed.
    Input details
    Add heading text and select the input details to display. The widget includes an option to group details by input name.
    Project details
    Add heading text and select the project details to display.
    Page break
    Add a page break widget where page breaks should appear between report sections.
  4. 4.
    Select Save.

Free Text Placeholders

Placeholder
Description
[[BB_PROJECT_NAME]]
The project name.
[[BB_PROJECT_OWNER]]
The project owner.
[[BB_PROJECT_DESCRIPTION]]
The project short description.
[[BB_PROJECT_INFORMATION]]
The project information.
[[BB_PROJECT_LOCATION]]
The project location.
[[BB_PROJECT_BILLING_MODE]]
The project billing mode.
[[BB_PROJECT_DATA_SHARING]]
The project data sharing settings.
[[BB_REFERENCE]]
The analysis reference.
[[BB_USERREFERENCE]]
The user analysis reference.
[[BB_PIPELINE]]
The name of the pipeline.
[[BB_USER_OPTIONS]]
The analysis user options.
[[BB_TECH_OPTIONS]]
The analysis technical options. Technical options include the TECH suffix and are not visible to end users.
[[BB_ALL_OPTIONS]]
All analysis options. Technical options include the TECH suffix and are not visible to end users.
[[BB_SAMPLE]]
The sample.
[[BB_REQUEST_DATE]]
The analysis request date.
[[BB_START_DATE]]
The analysis start date.
[[BB_DURATION]]
The analysis duration.
[[BB_REQUESTOR]]
The user requesting analysis execution.
[[BB_RUNSTATUS]]
The status of the analysis.
[[BB_ENTITLEMENTDETAIL]]
The used entitlement detail.
[[BB_METADATA:path]]
The value or list of values of a metadata field or multi-value fields.

Metadata Model

Workflow.cwl (code)

The Common Workflow Language main script.

Nextflow.config (code)

The Nextflow configuration settings.

Main.nf (code)

The Nextflow project main script.

+ New File (code)

Multiple files can be added to make pipelines more modular and manageable.

Compute Nodes

For each process defined by the workflow, ICA will launch a compute node to execute the process.
  • For each compute type, the standard (default) or economy tiers can be selected, which corresponds to AWS on-demand or spot instance types, respectively.
  • Compute nodes will have 2TB of local scratch storage mounted at /scratch
  • Sizes of compute nodes can be specified--see table below
  • The default size of a compute node, if a type is not specified, is standard-small

Compute Types

Daemon sets and system processes consume approximately 1CPU and 2GB Mem from the base values shown in the table. Consumption will vary based on the activity of the pod.
Compute Type
CPUs
Mem (GB)
Nextflow (pod.value)
CWL (type, size)
standard-small
2
8
standard-small
standard, small
standard-medium
4
16
standard-medium
standard, medium
standard-large
8
32
standard-large
standard, large
standard-xlarge
16
64
standard-xlarge
standard, xlarge
standard-2xlarge
32
128
standard-2xlarge
standard, 2xlarge
hicpu-small
16
32
hicpu-small
hicpu, small
hicpu-medium
36
72
hicpu-medium
hicpu, medium
hicpu-large
72
144
hicpu-large
hicpu, large
himem-small
8
64
himem-small
himem, small
himem-medium
16
128
himem-medium
himem, medium
himem-large
48
384
himem-large
himem, large
himem-xlarge
96
768
himem-xlarge
himem, xlarge
hiio-small
2
16
hiio-small
hiio, small
hiio-medium
4
32
hiio-medium
hiio, medium
fpga-small[^1]
8
122
fpga-small
fpga, small
fpga-medium
16
244
fpga-medium
fpga, medium
fpga-large
64
976
fpga-large
fpga, large
❗️ The compute type "fpga-small" is no longer available.

Start a New Analysis

Use the following instructions to start a new analysis for a single pipeline.
  1. 1.
    Select a project.
  2. 2.
    From the project menu, select Flow > Pipelines.
  3. 3.
    Select the pipeline to run.
  4. 4.
    Select Start a New Analysis.
  5. 5.
    Configure analysis settings. See Analysis Properties.
  6. 6.
    Select Start Analysis.
  7. 7.
    View the analysis status on the Analyses page.
    • Requested—The analysis is scheduled to begin.
    • Awaiting Input—The input file download is in progress.
    • In Progress—The analysis is in progress.
    • Succeeded—The analysis is complete.
    • Failed and Failed Final—The analysis has failed or was aborted.
  8. 8.
    To end an analysis, select Abort.
  9. 9.
    To perform a completed analysis again, select Re-run.
Alternatively, you can start a new analysis from Projects > <Your_Project> > Flow > Analyses
  1. 1.
    Select New Analysis
  2. 2.
    Select Pipeline
  3. 3.
    Configure analysis settings. See Analysis Properties.
  4. 4.
    Select Start Analysis.

Analysis Properties

The following sections describe the analysis properties that can be configured in each tab.

Analysis

The Analysis tab provides options for configuring basic information about the analysis.
Field
Entry
User Reference
The unique analysis name.
User tags
One or more tags used to filter the analysis list. Select from existing tags or type a new tag name in the field.
Entitlement Bundle
Select a subscription to charge the analysis to.
Input Files
Select the input files to use in the analysis. (max. 50,000)
Settings
Provide input settings.

View Analysis Results

You can view analysis results on the Analyses page or in the output_folder on the Data page.
  1. 1.
    Select a project, and then select the Flow > Analyses page.
  2. 2.
    Select an analysis.
  3. 3.
    On the Result tab, select an output file.
  4. 4.
    To preview the file, select the View tab.
  5. 5.
    Add or remove any user or technical tags, and then select Save.
  6. 6.
    To download, select Schedule for Download.
  7. 7.
    View additional analysis result information on the following tabs:
    • Details—View information on the pipeline configuration.
    • Logs—Download information on the pipeline process.
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Last modified 1mo ago