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Bioinformatics Analysis
Video Transcript


SC2 AMD Bioinformatics Analysis Transcript:

In this video we will review:

•    Starting a Pipeline Run
•    Monitoring a Pipeline Run
•    Releasing the Pipeline Run Analysis


New Updates: LIMS Lite is a software platform under active development. There may be small differences between the software as displayed in the video and the live version. Primary functionality of features covered in this video are current. For any additional questions on the differences, please reach out directly to the LIMS Lite team.

Starting a Pipeline Run

Once you reach the last step of your workflow, you may download the workflow sample sheet to your computer’s downloads folder.

Click ‘Finish Workflow’.

Load the Sample Sheet file onto your instrument, which will automatically rename the sample sheet appropriately, and add it to the run folder with your .fastq files

Once ready to begin the pipeline run, drop the entire run folder into the directory that Site Connector has been configured to watch.

If storage space is an issue, you may create a new directory as the ‘Run’ folder, and copy over the directory containing the .fastq files, Sample Sheet, and finally the RTA Complete file. 

If Site Connector is already running in the background, it will kick of the pipeline run as soon as it sees the new run files in the watched directory.

If Site Connector is not yet running, open Command Prompt, and enter the following commands and click Enter:

cd C:\Program Files (x86)\LIMSLite\LIMSLite.SiteConnector

SiteConnector-cli start 

Monitoring the Pipeline Run

To monitor your pipeline run in LIMS Lite, click on the Bioinformatics Analysis tab and then on Existing Pipeline Runs.

Under ‘Status’ will display the status of each existing pipeline run.

‘Pipeline Started’ denotes a run that has been kicked off and is currently running.

You may choose to log into Nextflow tower to monitor the status of your pipeline run.

For information on how to get started with Nextflow Tower, please refer to Appendix A of the LIMS Lite SARS-CoV-2 User Guide.

Here you can see all former and current run statuses.

Scroll Down to see details on run successes and failures.

‘Pipeline Finished’ displays after a pipeline run has completed and is ready to be analyzed.

Click on the ‘Continue’ button to access the Pipeline Analysis page.

Here you will see launch and completion dates of the pipeline run, as well as all samples included in the workflow.

Click on the ‘View Quality Control Metrics’ button to view quality metrics for each sample.

Fail Run and Release Run buttons are displayed at the bottom of the page.

If the run is acceptable to be released for data sharing or reporting purposes, click on ‘Release Run’.

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