February 26, 2019, Tuesday

• EMS/BSA workflow
  • Testing with users data
    • Failed due to long alignment time with Bowtie2, reads aligned but no time to merge
    • Solution to this?
      • Use CSHL server? Slow in data transfer, build an app to copy the data with iRODS, Need to allow text box input? Or allow multiple text boxes like multiple inputs?
      • Split read files and merge?
      • Assign more processors? Seems like there are more than 16 processors in one node but need to test, Stampede2 is under maintenance today
      • Use DE to run alignment? Need to optimize the workflow since the alignment part also did Picard
  • Optimizations
    • We might want to separate the bcftools_call app into several apps, so does the ems_filter app
• Encode Chipseq workflow
  • Failed with problemed data, some files are over 3 GB but some are less than 1 GB, why?
  • Testing with Sorghum data but Stampede2 is under maintenance today
• SciApps bugs
  • Index of 0
  • Workflow json with extra infos, can we remove them?