Quick Start

Quick Start Guide

The Heme pipeline may be executed using a local DRAGEN server or on a local computer which launches the analysis in the ICA cloud environment.

Table 1. Release Information

Execution Environment	software version	Client program	location	Note
Local Dragen Server	4.4.4.42	run_Heme_WGS_TO_${software_version}.sh	/usr/local/bin	See server installation section of this guide
ICA	adbdfbec-76ea-4cf9-a762-ce8c2bac6a52	icav2	ICA Pipelines	See cloud set up section of this guide

• ${software_version} is used to represent the software version number in the Table 1 above. Similarly, ${CLI_program} is used to indicate the client program name in this document.

Run analysis on a local DRAGEN Server

The command line program may be used to launch an analysis by using the ${CLI_program} with the appropriate options.

start from bcl

  ${CLI_program} --help # list all supported parameters
  ${CLI_program} --runFolder /staging/input-folder \
  --sampleSheet SampleSheet.csv \
  --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.

  ${CLI_program} --inputFolder /staging/input-folder-1,/staging/input-folder-2 \
  --sampleSheet /staging/output-folder \
  --analysisFolder /staging/utput-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 ICA using the icav2 client

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

  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 ICA using UI

The same analysis example above may be completed using the ICA UI by logging into the appropriate domain of your company and project where the Heme pipeline is set up. Find more information in the ICA Cloud App Launch Guide.