File Changes for ceisenhart

v336_preview2 to v336_base (2016-07-18 to 2016-07-25) v336

• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 6, context: html, text, full: html, text
    1f2603cbaeb38d6e465a8cfdde8fef88e751b5f1 Fri Jul 8 07:18:47 2016 -0700
    Passing assay into a library function for a new trimming step.
    
  • lines changed 4, context: html, text, full: html, text
    e03dc8b59d956f25ff3c2617ffaf60c57a23be8b Fri Jul 8 10:54:30 2016 -0700
    Fixing up the cutadapt call, need a .fastq before the .gz, which is done now with a symbolic link
    
• src/hg/cirm/cdw/cdwManiFastqToKallisto/cdwManiFastqToKallisto
  • lines changed 191, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/cdwManiFastqToKallisto/makefile
  • lines changed 6, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 26, context: html, text, full: html, text
    3b1d0cf233b3e801f1cc07fa52813ad06562938a Fri Jul 8 07:19:19 2016 -0700
    Putting a cutadapt call into the pipeline for longRNASeq data types.
    
  • lines changed 11, context: html, text, full: html, text
    e03dc8b59d956f25ff3c2617ffaf60c57a23be8b Fri Jul 8 10:54:30 2016 -0700
    Fixing up the cutadapt call, need a .fastq before the .gz, which is done now with a symbolic link
    
  • lines changed 77, context: html, text, full: html, text
    e40e0ad96f119b8756b92a8cf483d6869773acc3 Wed Jul 13 09:58:19 2016 -0700
    Adding in a cutadapt step to remove poly A tails which were gunking up the pipeline at the BWA step, refs #17334
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 191, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/makefile
  • lines changed 6, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244