Contributing¶

# Install dependencies
pixi install

# Download test data
pixi run dl-test-data

# Set up tools
pixi run setup-tools

git checkout -b feature/my-new-feature

pixi run fmt

# Dry run
pixi run dry-run

# Full test (requires GPU)
pixi run test

pixi run dag

rule example_rule:
    """
    Brief description of what the rule does.
    Include any important notes about behavior.
    """
    input:
        bam=rules.previous_rule.output.bam,
    output:
        tsv=os.path.join(outdir, "path", "{sample}", "{sample}.output.tsv.gz"),
    log:
        os.path.join(outdir, "logs", "example_rule", "{sample}"),
    params:
        src=SCRIPT_DIR,
        param_name=config.get("param", "default"),
    threads: 4
    shell:
        """
        command --input {input.bam} --output {output.tsv}
        """

#!/usr/bin/env python
"""
Script description.

Usage:
    python script.py --input file.bam --output file.tsv
"""
import argparse
import pysam
import pandas as pd


def process_bam(input_path, output_path):
    """
    Process BAM file and write results.

    Args:
        input_path: Path to input BAM file.
        output_path: Path to output TSV file.
    """
    # Implementation
    pass


def main():
    """Main entry point."""
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("--input", required=True, help="Input BAM file")
    parser.add_argument("--output", required=True, help="Output TSV file")
    args = parser.parse_args()

    process_bam(args.input, args.output)


if __name__ == "__main__":
    main()

# Description of this section
section:
    # What this parameter controls
    parameter: value

rule my_rule:
    """
    Short description of the rule.

    Longer description if needed, explaining:
    - Input requirements
    - Output format
    - Any special behavior
    """

pixi run test

pixi run snakemake <rule_name> --cores 4 --configfile=config/config-test.yml

pixi run snakemake -n --configfile=config/config-test.yml

feat: Add read length distribution rule

- Add get_read_lengths.py script
- Add read_length_distribution rule to aatrnaseq-qc.smk
- Update pipeline_outputs() to include new output

git push origin feature/my-new-feature

## Description
Brief description of changes.

## Type of Change
- [ ] Bug fix
- [ ] New feature
- [ ] Documentation update
- [ ] Refactoring

## Testing
How was this tested?

## Checklist
- [ ] Code follows style guidelines
- [ ] Snakemake files formatted (`pixi run fmt`)
- [ ] Documentation updated
- [ ] Tests pass locally