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Import a Nextflow Pipeline

Bioinformaticians can import and configure Nextflow pipelines 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 Nextflow 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.
  • The default Badge is set to Nextflow.
  • Next, enter the Tags for your pipeline, and input at least one Key and Value. For example (I), you can tag it as Pipeline (for Key) and enter the name of your nf-core pipeline, like nf-core/bactmap (for Value).
  • Finally select the Category to which your nf-core pipeline belongs from the options provided in the drop-down menu. (e.g.(I) Genomics)

Step 2: Source

  • The default repository Source is Git
  • Enter the source location under Repo e.g.(I) https://github.com/nf-core/bactmap.git
  • Provide the Revision parameter to be cloned (e.g.(I) HEAD, Branch Name, Tag as in: 1.0.0) and select the Nextflow Version from the drop-down menu (the default is the latest available version. You can also select the version that applies to your pipeline).

Step 3: Datasets

  • Select Add New Dataset. In the drop-down, Search for the name of the dataset you'd like to connect to your pipeline.(e.g.(I) refdata-1)
  • Add more datasets as required and click Next.

Step 4: Parameters

  • For each parameter that you'd like to add for your pipeline, Name it, select the Type from the drop-down menu (String, Integer, Boolean or File), and add text under Help to describe what the parameter is meant for.

  • If your pipeline configuration requires the user to upload an input file, your first parameter may be:

    • Name: Input CSV
    • Type: File

  • On selecting File, you will be prompted to choose between two options: based on whether you'd like the user to Upload or Browse for their 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. Next, fill-out the Help box by describing what this parameter is for.

    • If you select Browse, tick the checkbox Directory Only if the user needs to specify a directory for the input file. If not, you can also select the Dataset that the user may use for their input file. Fill the Help box by describing what this parameter is for.

  • Select Add New Parameter as required.

    • For parameters where the Type is String, Boolean, or Integer, you will be prompted to follow the same Browse steps as above to specify the dataset.
    • Additionally, 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 example (I), if your pipeline requires you to upload a pre-attached dataset, like a reference map, then your Add New Parameter fields might look like this:

    • Name: Reference
    • Type: File
    • Browse or Upload: Browse
    • Directory Only: No
    • Dataset: Name of your attached dataset (e.g.(I) refdata-1)

Step 5: Advanced

  • Under Advanced, specify the environment variables (Env) and the arguments (Args) that need to be passed to validate your pipeline's input parameters.

  • Enter the Key and Value for each. For example (I), Args can be your pipeline parameters.

    • Key: Reference | Value: Reference
    • Key: Input | Value: Input CSV

  • Optional: If you know the nextflow configuration, provide the Nextflow Config of the pipeline in the text box.

Step 6: Visualization

  • Select Add New Visualization App.
  • Select the Name of your visualization app from the drop-down menu.
  • Enter the Display Name for the visualization app.

Step 7: Permission

  • Specify permissions for each service given in the window.
  • For example (I), check whether the user has permission to View, Check/Edit, or Delete each service (S3, Batch, and Logs)

Step 8: 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 Nextflow Pipeline.
  • Proceed to Version and Publish your pipeline.