ICA Cloud App

Requirements

Analysis on ICA requires an account with a valid subscription and a project with the following configuration.

Manual Launch

How to Set up Project

1. Create a Project: Project can be specific for the DRAGEN Heme WGS Tumor Only v4.4.4 Pipeline or it can contain multiple Pipelines and/or Tools. For information on creating Projects, refer to the Projects section in Illumina Connected Analytics help. ICA standard storage is used by default as soon as the Project is saved. To connect a different storage source, set it up before creating your Project. For details and options, refer to the Storage section in Illumina Connected Analytics help.

2. Edit Project and Add Bundle: Edit the Project and add the bundle titled, "Heme WGS TO v4.4.4 (XX)." XX is a 2-letter code designating the region from which you are launching the analysis. Adding the Bundle automatically adds the pipeline and associated resource files and datasets to the Project. For information on Bundles, refer to the Bundles section in Illumina Connected Analytics help. After adding the Bundle to the Project, an example dataset becomes available in the Demo_Data folder for the Project.

3.  Upload the sequencing data: For information on viewing and uploading data, refer to the Data section in Illumina Connected Analytics help.

4. Start Analysis: In the Project, navigate to Pipelines, select the Heme WGS TO v4_4_4_x  Pipeline, and then select  "Start New Analysis". Set up the new analysis by configuring the parameters listed in the table below. When the required files are completed, start analysis.

5. Download Results: After analysis is complete, navigate to results in the configured output location.

Please see the Illumina Support Shorts for guidance on how to set up and run DRAGEN Heme WGS Tumor Only analysis on ICA.

Analysis Parameters on ICA

To launch an analysis via the ICA user interface, configure a DRAGEN Heme WGS Tumor Only pipeline analysis with the following parameters.

Parameter Name	Description
User Reference	The analysis run name
User Tags	Text labels to help index the analysis.
Notify me when task is completed	Option to receive an email notification when analysis is complete.
Output Folder	The path to the analysis output folder. The default path is the project output folder.
Entitlement Bundle	Automatically populated from the project details.
Samplesheet	Select a sample sheet in CSV format for the analysis.To note: Sample Sheet selection is optional if starting from a run folder, and required when submitting a FASTQ folder.
Input Directory	The run folder or FASTQ folder that contains files to analyze.
Input Type	Select input type of analysis will perform on. Options to select include bcl, fastq, bam and cram
Sample or Pair IDs	Optional subset of Sample IDs or Pair IDs to analyze.
Reference Genome	Select the reference genome. hs37d5_chr is the hg19 reference genome with the Chromosome Y PAR masked. It includes the NC_012920 mitocondria genome. The contigs have the chr prefix added, but without the native alternate loci names.
Enable Ora Compression	Enable Ora Compression (True or False). Only applicable when Input Type is bcl
Enable Post Processing	Enable Post Processing (True or False) to run custom scripts at the end of pipeline
Storage Size	The storage size to allocate for the analysis. The default and recommended value is Large.
Custom Parameters Config File	Optional. Select Custom Parameters Config File that override default config
Custom Resources Directory	Optional. Select Custom Resources Directory to use with Custom Parameters Config File
CAUTION - This parameter ...	Optional. Those configuration with this comment is only applies to auto-launch DRAGEN Heme WGS Tumor Only analysis from FASTQs after BCL. Please don't set it if start analysis from ICA UI

For information about using pipelines, refer to Illumina Connected Analytics support site page.