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

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

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