Ready to Run Pipelines

Running Pipelines from the Launchpad

1. Select Pipelines from the Navigator Menu on the left.
2. Click on the Launchpad tab.
3. Use Search to find the required workflow. For example, to find genomics pipelines that analyze DNA Sequencing datasets, search using terms like "sarek" or "dna".
4. Alternatively, users can Filter workflows available on Quark by Type or Category. Selecting Type from the drop-down menu allows users to select between nf-core or AWS Healthomics pipelines. Selecting the Category option displays different multi-omics workflow categories (Genomics, Proteomics, Transcriptomics, and so on).
5. Sort results by Name or version (Last Release) using the Sort By drop-down.
6. Select the required pipeline and click Run. The dashboard opens to the About page, which lists all the Input Parameters or fields required to run that particular pipeline.
7. The Run Pipeline tab prompts users to to name their run and fill out all input parameters.
8. Refer to the About tab and upload your sample datasheets in the prescribed format. The About tab further specifies the type of input parameters and file types supported for that pipeline.
9. Input other parameters from respective drop-down menus, and click Review.
10. Review all the input parameters (such as the uploaded file(s), input and output parameters), and Run the pipeline.

Viewing Results of Pipeline Runs

Users can retrieve the results of their pipeline runs and run comprehensive secondary data analyses using Quark's Vizapp.

Quark's Vizapp is an intuitive interface that enables users to directly visualise the results of their secondary data analyses, without requiring coding or bioinformatics expertise.

The following sections describe how to retrieve individual run results, and how to use Vizapp features for accessing in-depth secondary data analysis insights.

Retrieving Results of Pipeline Runs

1. Select Pipelines from the Navigator pane on the left, and click the Runs tab.
2. Use the Search bar to retrieve your run. Check the Status. If marked Complete, select your Run to open it.
3. The dashboard displays the following details of the Run:
   • Summary gives details of the runtime, the cost, and a link to View Samples under the sub-heading Analytics
   • Results allows users to download individual output files (for example MultiQC reports, variant annotation, variant calling files, etc.)
   • Input summarizes the input parameters given at the time of launching the run.
   • Log provides a timeline for each tool deployed.
   • About gives an overview of the pipeline deployed, its input requirements, and output formats.
4. For easier visualisation of secondary data analysis results, select the Summary tab, and click on the link to View Samples which loads after the pipeline run Status is Complete. This opens the Vizapp dashboard.

Using Vizapp to Visualize Pipeline Results

Quark's Vizapp is an intuitive interface that enables users to directly visualise the results of their secondary data analyses, without requiring coding or bioinformatics expertise.

Users can use the Vizapp for retrieving details of their secondary data analysis. The Vizapp Dashboard displays the following:

• Reports links directly to the pipeline's workflow management system report (e.g. to a Nextflow report) that provides details of the Run's logistics, such as resources allocated to each tool, the project directory path, pipeline version, etc.
• MultiQC aggregates all samples and associated metadata, enabling data retrieval and reusability