feltus/OSG-GEM

Added support for STAR read alignment software

update fasta_adapter.txt with new illumina adapter sequences

Added support for single end reads. User may select single or paired … …

…end reads as input

Added Log Merge Script to workflow. In addition to all standard outpu… …

…t files, a report of trimming and alignment statistics, QC_Report.tab, will be present in outputs directory

Updated Hisat2 Software. Temporarily transferring precompiled softwar… …

…e package to Compute nodes instead of using OASIS module

Added support for multiple inputs and a GEM merge at the end. Simplie… …

…d workflow by removing 3rd dax level (requires Pegasus 4.7)

Delete perl_cufflinks_parse.txt

Delete trimmomatic-0.33.jar

Delete trimmomatic-0.33.jar

Updated Trimmomatic Software and Hisat/Tophat Commands

Trimmomatic output in separate files, improved handling of annotation… …

… file and config checks

Added Test Input Files

Added StringTie task-files

Moved to new version in OASIS, added ref prefix functionallity

Added conf file and initial support for hisat2

Removed old splitter

Changes discussed at OSG all hands meeting. New faster splitter.

added files