feltus/OSG-GEM

Enabled the workflow to be executed on Jetstream

Added option to control memory allocation

Fixed typo in site catalog

Switched to wget

Added check for pigz

Request 2 GB RAM

Improved output dir message

Ignore old sites.xml

Make sure sites.xml is generated once and only once with the correct … …

…values

Switching back to wget

Moved SRA download jobs to vanilla universe

Merge pull request #7 from feltus/spficklin-patch-1 …

Update README.md. Thanks Stephen!

Improved documentation regarding ssh key setup

Switched back to stashcp for data staging

Moved workflow to use /local-scratch filesystem

Fix for missing dataset problem

fixed hisat2 output naming

Fixed dep problem with subwf

Removed the need for LD_LIBRARY_PATH

Fixed SRA download (removed debug subsetting)

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

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

Added some OSG details

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

… file and config checks

Added stringtie

Fixes for output of hisat and determining if we have empty inputs

Moved to new version in OASIS, added ref prefix functionallity

Fixed merge bug

Added conf file and initial support for hisat2

Removed old splitter

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