Zippy modules

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