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Check Genome GTF Specifications

Process Details

  • Name: Check Genome GTF
  • Process UUID: 17fc7b1c-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process verifies the availability of specified genome and GTF annotation files and ensures they are accessible for downstream analysis. When files are not found locally, the process automatically downloads them from provided source locations, supporting multiple storage platforms including AWS S3, Google Cloud Storage, and standard web servers. The process creates symbolic links to make the files available in the working directory and handles compressed files by automatically decompressing them when needed.

This process is implemented in Bash.

Key Functionality

  • File Availability Check: Verifies whether specified genome FASTA and GTF annotation files exist in the local environment
  • Multi-Platform Download: Automatically downloads missing files from AWS S3, Google Cloud Storage, or HTTP/HTTPS sources using appropriate tools (aws s3, gsutil, or wget)
  • File Preparation: Creates symbolic links to downloaded files and automatically decompresses gzipped files to ensure compatibility with downstream processes

Input/Output Specification

Inputs

This process does not require direct file inputs but depends on configuration parameters that specify file locations and sources.

Outputs

  • genome

    • Description: Reference genome sequence file made available for downstream processes
    • Format: FASTA

  • gtfFile

    • Description: Gene annotation file containing transcript and exon information
    • Format: GTF

References & Resources

  • Tool Documentation: This process uses standard system tools (wget, aws s3, gsutil) and does not require additional documentation beyond standard command references