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Import a WDL Pipeline

Bioinformaticians can import and configure Workflow Description Language (WDL) workflows by selecting the My Pipelines tab and clicking the Import Pipeline button on the top-right corner of the dashboard.

In the Select the Type window, click on WDL and then Continue to follow these steps.

Step 1: General

  • Name your pipeline and provide a brief text summary.
  • Under About, you can import a markdown file that provides a detailed summary of your pipeline.
  • Type the Badge name that you'd like to be displayed for your pipeline, e.g. WDL.
  • Next, enter the Tags for your pipeline, with at least one Key and Value. For example (I), you can tag it as Pipeline (for Key) and enter the name of your WDL pipeline, like biowdl-BamMetrics (for Value).
  • Finally select the Category to which your Bio-WDL pipeline belongs from the options provided in the drop-down menu (e.g.(I) Others).

Step 2: Source

  • The default repository Source is Git
  • Under Repo, enter your GitHub source location of the WDL workflows. (download the latest wdl files to your GitHub repository and enter the source location accordingly).
  • For public repos, provide the HTTPS repository URL (https://github.com/my-org/my-repo.git). For private repos, provide the SSH format repository details (git@github.com:my-org/my-repo.git)
  • Your Repo should be valid, starting with either "git@github.com:" or "https://github.com/" and ending with ".git"
  • Provide the Revision parameter to be cloned and enter the Workflow Entry Point or the directory location of your WDL file path (a valid path that does not start with / and ends with .wdl (e.g., folder/file.wdl).)

Step 3: Parameters

  • Select Add New Parameter.
  • For each parameter that you add for your pipeline, Name it, selecting the Type from the drop-down menu (String, Integer, Boolean or File), and add text under Help to describe what the parameter is.
  • If your pipeline configuration requires file uploads, select the parameter Type as File.

  • On selecting File, you will be prompted to choose between two options: based on whether you'd like to Upload or Browse for the file input.

    • If you select Upload, specify the file extension or Supported File Type from the drop-down menu. If, for example, you select .csv, you can enter one or more Header and Sample for your pipeline validation. Other file-types like .dict or .bai will not need additional definitions. Next, fill-out the Help box by describing what this parameter is.

    • If you select Browse, tick the checkbox Directory Only if the user needs to specify a directory for the input. If not, you can also select the Dataset to be used from the drop-down menu. Fill the Help box by describing what this parameter is for.

  • Select Add New Parameter as required.

    • For parameters where the Type is String, or Integer, you will be prompted to select the Field Type for each parameter. Choose based on whether the pipeline's user can Input their value or select them from a list of Dropdown values that you specify.
    • For parameters where the Type is Boolean, specify the prompted Dropdown Values by selecting Add New for each Boolean value.

Step 4: Review

  • The final window prompts you to Review your pipeline specifications.
  • After reviewing, Submit your pipeline.
  • Under the My Pipelines tab, you will see your newly imported WDL Workflow.
  • Proceed to Version and Publish your pipeline.