Launch pipelines

Launchpad

Each workspace has a Launchpad that allows users to easily create and share Nextflow pipelines that can be executed on any infrastructure supported by the Platform, including all public clouds and most HPC schedulers. A Launchpad pipeline consists of a pre-configured workflow repository, compute environment, and launch parameters.

Users can create their own pipelines, share them with others on the Launchpad, or tap into over a hundred community pipelines available on nf-core and other sources.

Advanced

Adding a new pipeline is relatively simple and can be included as part of the demonstration. See Add a Pipeline.

Launch the nf-core/rnaseq pipeline

1. Go to Launchpad

Navigate to the Launchpad in the seqeralabs/showcase workspace and select Launch next to the nf-core-rnaseq pipeline to open the launch form.

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2. Nextflow parameter schema

When you select Launch, a parameters page is shown to allow you to fine-tune the pipeline execution. This parameters form is rendered from a file called nextflow_schema.json which can be found in the root of the pipeline Git repository. The nextflow_schema.json file is a simple JSON-based schema describing pipeline parameters that allows pipeline developers to easily adapt their in-house Nextflow pipelines to be executed via the interactive Seqera Platform web interface.

See the "Best Practices for Deploying Pipelines with the Seqera Platform" blog for further information on how to automatically build the parameter schema for any Nextflow pipeline using tooling maintained by the nf-core community.

3. Parameter selection

Adjust the following Platform-specific options if needed:

• Workflow run name:

  A unique identifier for the run, pre-filled with a random name. This can be customized.

• Labels:

  Assign new or existing labels to the run. For example, Project ID or genome version.

Each pipeline including nf-core/rnaseq will have its own set of parameters that need to be provided in order to run it. The following parameters are mandatory:

• input:

  Most nf-core pipelines have standardized the usage of the input parameter to specify an input samplesheet that contains paths to any input files (such as FastQ files) and any additional metadata required to run the pipeline. The input parameter can accept a file path to a samplesheet in the S3 bucket selected through Data Explorer (such as s3://my-bucket/my-samplesheet.csv). Alternatively, the Seqera Platform has a Datasets feature that allows you to upload structured data like samplesheets for use with Nextflow pipelines.

  For the purposes of this demonstration, select Browse next to the input parameter and search and select a pre-loaded dataset called "rnaseq_samples".

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  Advanced

  Users can upload their own samplesheets and make them available as a dataset in the 'Datasets' tab. See Add a dataset.

• outdir:

  Most nf-core pipelines have standardized the usage of the outdir parameter to specify where the final results created by the pipeline are published. outdir must be different for each different pipeline run. Otherwise, your results will be overwritten. Since we want to publish these files to an S3 bucket, we must provide the directory path to the appropriate storage location (such as `s3://my-bucket/my-results).

  For the outdir parameter, specify an S3 directory path manually, or select Browse to specify a cloud storage directory using Data Explorer.

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Users can easily modify and specify other parameters to customize the pipeline execution through the parameters form. For example, in the Read trimming options section of the parameters page, change the trimmer to select fastp in the dropdown menu, instead of trimgalore, and select Launch button.