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Running the Workflow Test

Before running your own data, test the workflow with our provided test dataset to verify your system configuration and dependencies. This test run serves as a software validation tool to ensure that:

  • All dependencies are correctly installed and accessible
  • Your system meets the minimum requirements
  • The workflow can execute successfully from start to finish
  • Your computing environment is properly configured

Tip

The test dataset is intentionally small and simplified for quick validation. It contains downsampled data that is not representative of real experimental results. Do not use the test outputs as an example of what your actual analysis results should look like.

For real example datasets and expected outputs from actual experiments, please visit the ScaleBio Support Website where we provide comprehensive example datasets with detailed explanations of the results and interpretation guidelines.

Quick Start

# Download test data
aws s3 sync s3://scale.pub/testData/rna/202504_quantumV1/fastq fastq --no-sign-request
aws s3 sync s3://scale.pub/testData/rna/GRCh38_chr20_genome GRCh38_chr20_genome --no-sign-request

# Run workflow
nextflow run /PATH/TO/ScaleRna/ \
  -profile docker \
  -params-file /PATH/TO/ScaleRna/docs/examples/runParams.yml \
  --genome GRCh38_chr1_genome/grch38.chr1.json \
  --fastqDir fastq \
  --outDir /PATH/TO/OUTPUT_DIR

Test Dataset Details

  • Data: Downsampled Quantum ScaleRNA v1 experiment
  • Genome: GRCh38 chromosome 20 subset
  • Size: ~500 MB input, ~2 GB output
  • Pipeline Run Time: About a minute
  • Purpose: System validation only (not realistic dataset)

Need Help?

For more information, please contact support@scale.bio or visit our support website.