Quick Start

Quick Start Guide

HEME 4.4.4

Execution Environment	software version	Client program	location	Note
Local Dragen Server	4.4.4.62	run_Heme_WGS_TO_4.4.4.62.sh	/usr/local/bin	See Dragen Server
Platform Core	a11697ba-1144-4dc6-9e22-f21dff29f747		Platform Core Pipelines	See Cloud App
Platform Core	urn:ilmn:ica:pipeline:a11697ba-1144-4dc6-9e22-f21dff29f747#Heme_WGS_TO_v4_4_4_62	supported browser	Platform Core UI	See Launching Cloud Analysis

HEME 4.4.6

Execution Environment	software version	Client program	location	Note
Local Dragen Server	4.4.6.44	run_Heme_WGS_TO_4.4.6.44.sh	/usr/local/bin	See Dragen Server
Platform Core	13bdcb5a-ff43-4dd3-9bc7-1264f246c719	icav2	Platform Core Pipelines	See Cloud App
Platform Core	urn:ilmn:ica:pipeline:13bdcb5a-ff43-4dd3-9bc7-1264f246c719#Heme_WGS_TO_v4_4_6_44	supported browser	Platform Core UI	See Launching Cloud Analysis

<pipeline_run_script> is used to indicate the client program name in this document. Example, run_Heme_WGS_TO_4.4.4.62.sh for the HEME WGS T/O v4.4.4 pipeline.

Download, Install and Execute on a Local Server

The software may be downloaded and installed by following the installation guide. It may be executed using a local DRAGEN server or on a local computer which launches the analysis in the ICA cloud environment.

Run analysis on a local DRAGEN Server

The command line program may be used to launch an analysis by using the <pipeline_run_script> with the appropriate options.

start from bcl

<pipeline_run_script> --help # list all supported parameters
<pipeline_run_script> --inputType bcl \
--inputFolder /staging/input-folder \
--analysisFolder /staging/output-folder

start from one or more input folders when using FASTQ, BAM or CRAM files

Multiple folders may be specified as input folders in comma separated values when using FASTQ, BAM or CRAM files as input.

<pipeline_run_script> --inputType <fastq|bam|cram> \
--inputFolder /staging/input-folder-1,/staging/input-folder-2 \
--analysisFolder /staging/output-folder

Pressing Ctrl+C during a DRAGEN step stops the currently running analysis and might cause an FPGA error. To recover from an FPGA error, shut down and restart the server.

Run analysis on cloud using the icav2 client

Here is an example of starting an analysis using the Platform Core client by providing the necessary command parameters and specify a particuar storage size for analysis in cloud.

icav2 projectpipelines start nextflow ${PIPELINE_ID} \
--project-id ${ANY_PROJECT_ID} \
--storage-size Large \
-o json \
--input ${ANY_SAMPLE_SHEET} \
--input ${ANY_INPUT_DIR} \
--parameters inputType:'bcl' \
--parameters referenceGenome:'hg38' \
--parameters oraCompressionEnabled:'true' \
--parameters sampleIds:'1267-Prostate-Del-R1,741-Lung-SNV-R1' \
--user-reference ${ANY_USER_REFERENCE}

Run analysis on cloud using UI

The same analysis example above may be completed using the Platform Core UI by logging into the appropriate domain of your company and project where the Heme pipeline is set up.

Find more information in the Launching Cloud Analysis section of this guide.