# 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 Launch Analysis 1. **Create a Project:** Project can be specific for the DRAGEN Solid WGS Tumor Normal 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](https://help.ica.illumina.com/home/h-projects). > **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**](http://help.ica.illumina.com/home/h-storage)**.** 1. **Edit Project and Add Bundle:** Edit the Project and add the bundle titled, "Solid WGS TN 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](https://help.ica.illumina.com/home/h-bundles). > **After adding the Bundle to the Project, an example dataset becomes available in the Demo\_Data folder for the Project.** 1.  **Upload the sequencing data:** For information on viewing and uploading data, refer to the Data section in [Illumina Connected Analytics help](https://help.ica.illumina.com/project/p-data). 2. **Start Analysis:** In the Project, navigate to Pipelines, select the Solid WGS TN 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](#analysis-parameters-on-ica). When the required files are completed, start analysis. 3. **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 Solid WGS Tumor Normal analysis on ICA. ## Analysis Parameters on ICA To launch an analysis via the ICA user interface, configure a DRAGEN Solid WGS Tumor Normal 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 Solid WGS Tumor Normal 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](https://support.illumina.com/sequencing/sequencing_software/illumina-connected-analytics.html). For more information about using ICA and BaseSpace Sequence Hub or running a pipeline Analysis Software analysis on ICA, refer to the relevant support pages on the Illumina support site.