feltus/OSG-GEM

Format StringTie output for easy input into Ballgown R package

fixed GFF3 file identification so that the workflow does not fail to … …

…submit when a GFF3 is present in both the 'reference' and 'star_reference' directory

fixed reference identification message and added i2t.ctab and e2t.cta… …

…b as outputs of stringtie

Added support for STAR read alignment software

transfer i_data.ctab and e_data.ctab as output of workflow (all three… …

… *ctab files required for input into ballgown)

Transfer ctab files as output for downstream DEG analysis. Do not tra… …

…nsfer individual log files to output

use new Pegasus OASIS module

Small tweaks to reduce disk usage. Do not write unpaired fastq files … …

…or GTF files

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

Improved file system layout when running on Jetstream

Enabled the workflow to be executed on Jetstream

fixed tophat output naming

Added option to control memory allocation

Updated Hisat2 Software. Temporarily transferring precompiled softwar… …

…e package to Compute nodes instead of using OASIS module

Added check for pigz

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

…values

Moved SRA download jobs to vanilla universe

Fix for missing dataset problem

fixed hisat2 output naming

Fixed dep problem with subwf

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)

Delete old fastq-splitter

Updated Samtools

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

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

Added StringTie task-files

Moved to new version in OASIS, added ref prefix functionallity

fixed hisat2 merging support

Fixed merge bug

Added conf file and initial support for hisat2