RNA-seq Snakefile MultiQC Stacked Bar Chart Expression Module

[menoldmt]

RNA-seq Snakefile MultiQC Stacked Bar Chart Expression Module

Overview

This PR adds functionality to generate a stacked bar chart in MultiQC, visualizing normalized expression for user-defined regions from a GTF file. It includes new rules, configuration options, and tests.

Additions

1. Snakefile Rules:

   • Added rules in workflows/rnaseq/Snakefile for generating stacked bar charts.
   • Functions implemented in lib/multiqc.py.

2. Configuration:

   • Updated workflows/rnaseq/config/config.yaml to define user-specified regions for MultiQC output.

3. Tests:

   • Workflow Tests:
     • Added tests in test/lcdb-wf-test for validating MultiQC and Snakefile outputs.
     • New function validate_counts() in lib/common.py.
   • Module Tests:
     • Added tests in lib/test_suite.py for lib/multiqc.py functions.
     • Test files: normalized_counts.tsv, test_sampletable.tsv, test_featurecounts.tsv (in test/test_configs/).

Purpose

Enable region-specific expression visualization in MultiQC HTML output, for example, to evaluate the effectiveness of an RNA-protein binding process.

Validation

• Unit Tests: Ensure lib/multiqc.py functions work as expected.
• Workflow Tests: Validate Snakefile outputs and MultiQC integration using realistic test data.

Documentation

Relevant documentation is included in the Snakefile and library files.