# Launching Analysis

## UI Options

### Manual Launch of pipeline Analysis Software Analysis

To manually launch an analysis, configure a pipeline Analysis Software pipeline analysis run in ICA with the following parameters.

#### General

| Parameter Name | Description                                                                                                    | Required | Default               |
| -------------- | -------------------------------------------------------------------------------------------------------------- | -------- | --------------------- |
| User Reference | The custom name of the analysis for later identification.                                                      | Yes      | Empty                 |
| User Tags      | Tags for the analysis to help with categorization and identificaion, enhancing organization and searchability. | No       | Empty                 |
| Notification   | Add a user to be notified when the analysis completes.                                                         | No       | No user selected      |
| Output Folder  | The path to the analysis output folder.                                                                        | No       | Project output folder |

#### Input Files

| Parameter Name                | Description                                                                                                                            | Required | Default                         |
| ----------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | -------- | ------------------------------- |
| Samplesheet                   | The SampleSheet.csv for the analysis                                                                                                   | Yes      | SampleSheet.csv in Input Folder |
| Input Directory               | The input folder that contains \[bcl, fastq, bam, cram] files to analyze. Multiple input \[fastq, bam, cram] folders can be specified. | Yes      | No folder selected              |
| Custom Parameters Config File | The custom parameters config file for the analysis.                                                                                    | No       | No file selected                |
| Custom Resources Directory    | The custom resoruces directory used for the analysis.                                                                                  | No       | No folder selected              |

#### Settings

| Parameter Name         | Description                                                                         | Required | Default |
| ---------------------- | ----------------------------------------------------------------------------------- | -------- | ------- |
| Input Type             | The type of files in the Input Folder(s): bcl, fastq, bam, cram.                    | Yes      | bcl     |
| Reference Genome       | The reference genome used for the analysis: \[hs37d5\_chr, hg38].                   | Yes      | hg38    |
| Enable Ora Compression | Compress fastq files using ora compression. \[Only applies when Input Type is bcl]. | No       | true    |
| Enable Post Processing | Use the post-processing scripts at the end of the pipeline analysis.                | No       | false   |
| Sample IDs             | Optional subset of Sample IDs or Pair IDs to analyze. A comma-separated list.       | No       | Empty   |

#### Resources

| Parameter Name | Description                                                                         | Required | Default |
| -------------- | ----------------------------------------------------------------------------------- | -------- | ------- |
| Storage Size   | The storage size to allocate for the analysis. The minimum required value is Large. | Yes      | Large   |

Other available options for the storage size:

* "1.2TB" if option selected is Small
* "2.4TB" if option selected is Medium
* "7.2TB" if option selected is Large
* "16TB" if option selected is XLarge
* "32TB" if option selected is 2XLarge
* "64TB" if option selected is 3XLarge

> **Note:** It is recommended to reserve storage size twice the size of the BCL run folder, or the input fastq.gz or bam files, four times the size of the cram file (cram is 30-70% of the bam), and 8 times the size of the fastq.ora (fastq.ora is about 25% of fastq.gz).

For information about using pipelines, refer to the Illumina Connected Analytics documentation.