Launching Analysis

UI Options

Manual Launch of Heme pipeline Analysis Software Analysis

To manually launch an analysis, configure a Heme 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).

Using the icav2 client

Customer may use the icav2 client to launch analysis from the CLI. The specific parameters supported may be obtained from the Project Pipeline details under the XML configuration tab.

XML Configuration Parameters

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