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Merge Sample Orfs Specifications

Process Details

  • Name: merge_sample_orfs
  • Process UUID: f931t8tfdr34ktvh1hv7no6c64gbx2
  • Process Group: Annotation

Overview

This process consolidates ORF (Open Reading Frame) annotation files from multiple samples into a single unified file. This aggregation step is essential for comparative genomic analysis and downstream processing workflows where a comprehensive view of all identified ORFs across samples is required.

This process is implemented in Bash, which invokes a Python script for data merging operations.

Key Functionality

  • ORF Consolidation: Merges individual sample ORF annotation files into a single comprehensive dataset
  • Data Integration: Combines annotation information from multiple samples while maintaining sample-specific identifiers
  • Format Standardization: Ensures consistent formatting across merged ORF annotations for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • ORF Annotation File
    • Description: Tab-separated file containing ORF annotations from bacterial genome annotation (typically from Bakta or similar tools)
    • Format: TSV

Outputs

  • Merged ORF Annotations
    • Description: Consolidated tab-separated file containing all ORF annotations from input samples
    • Format: TSV

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on merge_sample.py