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Zippy modules

Wise, Aaron edited this page Aug 31, 2017 · 12 revisions

Here we list the current zippy modules and their file output formats. To use a module, type the name before 'Runner' as a stage into your proto.json. The names are case-insensitive.

Help on individual stages is now available directly from the command line. Try 'python zippy.py --help Runner

  • Bcl2FastQRunner
    • Outputs fastq
  • BWARunner
    • Outputs bam
  • BWAAlignStatsRunner: Performs various picard metrics
    • Outputs align_stats, insert_stats, insert_plot (pdf image)
  • DataRunner: Loads into the pipeline external data from a specified directory.
    • Outputs all data found in the specified directory. It assumes that all data files associated with a sample will have the sample name somewhere in the filename. The output type is taken from the file extension.
  • RSEMRunner: RNA quantification
    • Outputs rsem (a genes.results file)
  • MACSRunner: Peak calling
    • Currently returns no output (though it generates various peak-related files)
  • MarkDuplicatesRunner: Runs picard's markduplicates function
    • Outputs bam
  • SubsampleBAMRunner: Runs samtools view subsampling
    • Outputs bam
  • MergeBamRunner: Runs samtools merge. Currently many-to-one, but a many-to-fewer version is possible.
    • Inputs: samples: which sample names to merge from incoming stages
    • Outputs (one) bam
  • IndelRealignment: Runs Hygea. Experimental!
    • Outputs bam
  • Pisces: Runs... uh... you got this one. Experimental!
    • Outputs vcf
  • STAR:
    • Takes the 'args' parameter for command line arguments to be passed to STAR
    • Outputs bam
  • FastQC
    • Inputs: fastq
    • Outputs: produces statistical output, but currently returns no output to ZIPPY
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