eyrie-popup 0.1.0

Pipeline Output Processor and UPloader for Eyrie - parsing sequencing analysis results

Eyrie POPUP - Pipeline Output Processor and UPloader

A Python tool for processing pipeline outputs and uploading sequencing analysis results to the Eyrie database.

Features

• YAML Configuration: Flexible configuration format for describing analysis runs
• Multi-format Support: Parse FastQC, Krona, MultiQC, NanoPlot, and taxonomic abundance files
• Contamination Detection: Automatic flagging of potential contaminants
• API Integration: Direct upload to Eyrie database via REST API
• CLI Interface: Easy-to-use command line tool

Installation

cd tools/eyrie-popup
pip install -e .

Usage

Generate Configuration

Auto-generate a configuration file for a sample:

popup generate-config /path/to/analysis/results sample_id --output config.yaml

Upload Sample

Parse analysis results and upload to Eyrie:

popup upload --sample config.yaml --api http://localhost:8000/api --username admin --password admin

Use --dry-run to parse without uploading:

popup upload --sample config.yaml --dry-run --verbose

Test Connection

Test connection to Eyrie API:

popup test-connection --api http://localhost:8000/api --username admin --password admin

Configuration Format

The YAML configuration file describes the analysis run structure:

# Sample information
sample:
  sample_id: "barcode01"
  sample_name: "Sample_BC01"
  lims_id: "LIMS_BC01_001"
  barcode: "barcode01"
  sequencing_run_id: "RUN_2025_09_30"
  classification_type: "16S"  # or "ITS"

# Base directory containing all analysis outputs
base_path: "/path/to/analysis/results"

# Run directory name for file paths (defaults to sequencing_run_id if not specified)
run_directory: "test"

# Quality control files
fastqc:
  enabled: true
  directory: "fastqc"
  file: "barcode01_fastqc.html"

# Taxonomic classification plots
krona:
  enabled: true
  directory: "krona"
  file: "barcode01_krona.html"

# Nanopore-specific plots and statistics
nanoplot:
  unprocessed:
    enabled: true
    directory: "nanoplot_unprocessed"
    stats_file: "barcode01_nanoplot_unprocessed_NanoStats.txt"
    html_files:
      - "barcode01_nanoplot_unprocessed_NanoPlot-report.html"
      # ... additional HTML files
  processed:
    enabled: true
    directory: "nanoplot_processed" 
    stats_file: "barcode01_nanoplot_processed_NanoStats.txt"
    html_files:
      - "barcode01_nanoplot_processed_NanoPlot-report.html"
      # ... additional HTML files

# Analysis results
results:
  enabled: true
  directory: "results"
  rel_abundance_file: "barcode01_filtered.fastq_rel-abundance.tsv"

Supported File Types

• FastQC: HTML quality control reports per sample
• Krona: Interactive taxonomic classification plots
• MultiQC: Aggregated quality control reports
• NanoPlot: Nanopore-specific quality plots and statistics
• Taxonomic Abundances: Relative abundance TSV files
• Pipeline Files: Associated analysis outputs

Contamination Detection

The tool can automatically detect potential contaminants based on:

• Species names in a suspected contaminants list
• Abundance thresholds (e.g., >5% abundance)
• Custom contamination rules

API Integration

Samples are uploaded to Eyrie with:

• Quality control status (passed/failed/unprocessed)
• Statistical summaries
• File paths for visualization
• Taxonomic classification data
• Contamination flags

Development

Install development dependencies:

pip install -e ".[dev]"