feltus/OSG-GEM

Format StringTie output for easy input into Ballgown R package

Update README.md …

Update SSH key setup

exclude problematic compute sites from sites catalog

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

update fasta_adapter.txt with new illumina adapter sequences

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use new Pegasus OASIS module

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

…or GTF files

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Added support for single end reads.  In the config file, the user must specify whether input datasets contain single or paired-end reads.  A mixture of single and paired end reads cannot be used.

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

fixed tophat output naming

Update osg-gem.conf.example …

Lowered default memory request and removed SRA ID as second input(takes hours to download the input data, user's may not want this for quick test runs)

Updated Hisat2 Software. Temporarily transferring precompiled softwar… …

…e package to Compute nodes instead of using OASIS module

OSG-GEM Update …

Support added for:

-Processing multiple input datasets in a single workflow
-Downloading input data directly from NCBI SRA database

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Update submit …

Added LD library path for Pegasus 4.7.0dev

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added useful files directory

Update Documentation

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Update README.md

Increased default memory request

Delete old fastq-splitter

Delete perl_cufflinks_parse.txt