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pipeline

A modular, file-based analysis pipeline for NGS data

Notes:

  • This is the start of a basic processing pipeline

  • The pipeline starts from demultiplexed fastq files.

  • Modules will initially include

    • fastqc
    • cleaning with trimomatic
    • aligning to a reference with tophat

Each module will have a log file containing

  • name of module
  • command line
  • input files
  • start time
  • execution node
  • end time
  • output files

A separate trawler script will pick up the log files and parse them (could well fit in with our parallel filesystem walking code)

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A modular, file-based analysis pipeline for NGS data

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