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Download Build Sequential Mapping Indexes Specifications

Process Details

  • Name: Download_build_sequential_mapping_indexes
  • Process UUID: 8mPjid59F1qnA8NLp56EwnaX5qXYqh
  • Process Group: Index

Overview

This process manages the download and construction of sequential mapping indexes for bioinformatics workflows. It intelligently checks if the required mapping indexes (Bowtie2, Bowtie, and STAR) need to be downloaded or built, and handles the necessary directory management for these indexes. The process is designed to work with various data sources including S3 buckets, Google Cloud Storage, and direct downloads.

This process is implemented in Bash, which invokes external bioinformatics tools (Bowtie2, Bowtie, and STAR) for index generation.

Key Functionality

  • Conditional Index Building: Automatically determines which indexes need to be built based on sequential mapping configuration and existing file availability
  • Multi-source Data Handling: Supports downloading reference databases from S3, Google Cloud Storage, or direct HTTP sources
  • Index Management: Creates and manages Bowtie2, Bowtie, and STAR indexes with proper directory structure and symbolic linking
  • Intelligent Caching: Checks for existing indexes before rebuilding to optimize processing time

Input/Output Specification

Inputs

Required Inputs

  • genome

    • Description: Reference genome sequence file used for building mapping indexes
    • Format: FASTA

  • gtfFile

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

Outputs

  • commondb

    • Description: Common database directory containing reference data and resources
    • Format: Directory

  • bowtieIndex

    • Description: Bowtie alignment index files for the reference genome
    • Format: Bowtie Index

  • bowtie2index

    • Description: Bowtie2 alignment index files for the reference genome
    • Format: Bowtie2 Index

  • starIndex

    • Description: STAR aligner index files for the reference genome
    • Format: STAR Index

Parameters & Settings

This process uses parameters configured in the Sequential Mapping module and does not expose direct user-configurable parameters in the Foundry UI. Index building is controlled by the sequential mapping workflow configuration.

References & Resources

  • Tool Documentation: Contact the team for details on the index building scripts
  • Related Papers:
  • Bowtie2: Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-359. doi:10.1038/nmeth.1923
  • STAR: Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635