Batteries Included: Supercharging Bioinformatics Modules with Viash

TL;DR

Viash comes with powerful built-in features that would normally require significant additional coding: parallel batch processing for speed, container management for reproducibility, and integrated testing for reliability. These “batteries included” features save you from writing hundreds of lines of boilerplate code.

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Integrated Testing

The Testing Challenge in Bioinformatics

Traditional testing involves: - Writing test scripts - Managing test data - Setting up environments - Comparing expected vs. actual outputs

These steps are often skipped, causing fragile tools. Viash makes testing a first-class citizen.

Built-in Testing with Viash

Example test script test.sh:

#!/bin/bash

echo ">>> Testing $meta_functionality_name"
"$meta_executable"  --input "$meta_resources_dir/test.paired_end.sorted.bam"  --output "$meta_resources_dir/test.paired_end.sorted.txt"

echo ">>> Checking whether output is non-empty"
[ ! -s "$meta_resources_dir/test.paired_end.sorted.txt" ] && echo "File 'test.paired_end.sorted.txt' is empty!" && exit 1

echo ">>> Checking whether output is correct"

diff <(grep -v "^# The command" "$meta_resources_dir/test.paired_end.sorted.txt")    <(grep -v "^# The command" "$meta_resources_dir/ref.paired_end.sorted.txt") ||    (echo "Output file ref.paired_end.sorted.txt does not match expected output" && exit 1)

rm "$meta_resources_dir/test.paired_end.sorted.txt"

echo ">>> All tests passed successfully."

exit 0

Viash config addition:

name: samtools_stats
arguments:
  ...
test_resources:
  - type: bash_script
    path: test.sh
  - type: file
    path: test.paired_end.sorted.bam

Run tests with:

viash ns test -q samtools_stats

Why Viash Testing Is a Game-Changer

• Reproducibility: Tests run in the same environment as production
• CI/CD Friendly: Easily integrates into pipelines
• Version Control: Test code lives beside the component

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Parallel Processing

The Challenge

Bioinformaticians often need to process many samples with: - Resource tracking - Logging - Monitoring

Viash enables built-in batch processing.

The Viash Way: Parameter Lists

Example param_list.yaml:

- id: sample_1
  input: test.paired_end.sorted_1.bam
  output: test.paired_end.sorted_1.bam
- id: sample_2
  input: test.paired_end.sorted_2.bam
  output: test.paired_end.sorted_2.bam
- id: sample_3
  input: test.paired_end.sorted_3.bam
  output: test.paired_end.sorted_3.bam

Run it with:

nextflow run target/nextflow/samtools_stats/main.nf   --param_list param_list.yaml   -profile docker   -publish-dir test

Why Batch Processing with Viash Rocks

• Efficiency: No need to code parallelization logic
• Flexibility: Sample-specific parameters supported
• Simplicity: Easy YAML file defines all processing

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Container Management

The Reproducibility Problem

Containers solve environment drift, but are often: - Hard to configure - Hard to version - Hard to debug

Viash to the Rescue

Viash handles: - Dockerfile generation - Container build + caching - Volume mounting - Lifecycle management

Custom Docker snippet in config:

engines:
  - type: docker
    image: quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
    setup:
      - type: docker
        run: |
          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' |           sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

Inspect Dockerfile:

viash run src/config.vsh.yaml ---dockerfile

Debug mode:

viash run src/config.vsh.yaml ---debug

Why Viash Container Management Is a Game-Changer

• No Docker Knowledge Needed
• Consistent Environments Everywhere
• Transparent Versioning and Caching
• Multi-container Tech Support

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What’s Next?

In the next post, we’ll show how to combine Viash components into modular workflows, such as RNA-seq pipelines.

Check out the Viash documentation for more.