Commits for ceisenhart

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

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/cdwManiFastqToKallisto - lines changed 191, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwManiFastqToKallisto/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani - lines changed 191, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/makefile - 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.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 6, 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.
  
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 26, 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/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 11, 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/lib/cdwLib.c - lines changed 77, context: html, text, full: html, text