# ICA Cloud App ## Prerequisites To run analyses on Illumina Connected Analytics (ICA), you need: * An ICA account with a valid subscription * A project configured for the DRAGEN Solid WGS Tumor Normal Pipeline For general ICA documentation, refer to the [Illumina Connected Analytics Help](https://help.ica.illumina.com/). ## Launching Analysis Follow these steps to launch a DRAGEN Solid WGS Tumor Normal analysis on ICA: ### 1. Create a Project Create a new ICA Project (or use an existing one). The Project can be dedicated to the DRAGEN Solid WGS Tumor Normal v4.4.4 Pipeline or contain multiple pipelines and tools. 📖 For detailed instructions, see [Projects](https://help.ica.illumina.com/home/h-projects) in the ICA documentation. > **Note:** ICA standard storage is used by default when the Project is saved. To use a different storage source, configure it before creating your Project. See [Storage](https://help.ica.illumina.com/home/h-storage) for details. ### 2. Add Bundle to Project Edit the Project and add the bundle titled **"Solid WGS TN v4.4.4 (XX)"**, where XX is a 2-letter region code for your analysis location. Adding the Bundle automatically provisions: * The DRAGEN Solid WGS TN Pipeline * Associated reference files and resources * Demo data in the `Demo_Data` folder 📖 For more information, see [Bundles](https://help.ica.illumina.com/home/h-bundles) in the ICA documentation. ### 3. Upload Sequencing Data Upload your sequencing data (FASTQ, BAM, CRAM, or BCL files) to the Project. 📖 For upload instructions, see [Data](https://help.ica.illumina.com/project/p-data) in the ICA documentation. ### 4. Configure and Start Analysis 1. Navigate to **Pipelines** in your Project 2. Select the **Solid WGS TN v4\_4\_4\_x** Pipeline 3. Click **"Start New Analysis"** 4. Configure the parameters listed in the [Analysis Parameters](#analysis-parameters) section below 5. Click **Start** to launch the analysis ### 5. Download Results After analysis completion, navigate to the configured output folder to access and download your results. ## Analysis Parameters To launch an analysis via the ICA user interface, configure the DRAGEN Solid WGS Tumor Normal pipeline 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. **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 for analysis. Options include: `bcl`, `fastq`, `bam`, `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 Chromosome Y PAR masked. It includes the NC\_012920 mitochondria 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 overrides default config. | | Custom Resources Directory | Optional. Select Custom Resources Directory to use with Custom Parameters Config File. | | CAUTION - This parameter ... | Optional. This configuration only applies to auto-launch DRAGEN Solid WGS Tumor Normal analysis from FASTQs after BCL conversion. **Do not set this parameter when starting analysis from the ICA UI**. | *** For more information about using ICA and launching pipeline analyses, refer to the [Illumina Connected Analytics support page](https://support.illumina.com/sequencing/sequencing_software/illumina-connected-analytics.html). --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/setup.md?ask= ``` The question should be specific, self-contained, and written in natural language. 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