Increase bwa memory requirements

Increases memory requirements to 32 GiB. See #79

Increase memory requests

Applies lessons learned on GATK4 workflow to increase memory limits for parallelized steps

exome-seq memory allocation fixes

Fixes memory allocations in exome-seq map and sort steps

exome-seq GATK4 workflow

• Updates to build workflows under Pyhon 3
• Includes utility scripts for bespin-cli workflow/version/config loading
• Improvements for exomseseq GATK4 preprocessing workflow
  • Documents required secondaryFiles
  • adds variant calling step to gatk4-preprocessing
  • Provides examples for GATK4 tools
  • Reworks custom type schemas
  • tweaks memory requirements after running
• Adds exome-seq GATK4 workflow (subworkflows 02 and 03)
  • Adds necessary GATK4 tool definitions

v0.9.4

v0.9.4 GATK 4 Preprocessing Workflow

Exomseq combine reads

Unifys reads made up of multiple files: #60
Fixes FastQC memory allocation bug: #57

v0.9.2: Version 0.9.2: Updated exome-seq capture kit

- Updates capture kit to xGen
- Switches to decoy reference genome
- Reconfigures some output files

v0.9.1: Merge pull request #52 from Duke-GCB/exomeseq-study-size

• Optimizes exome-seq interval list generation
• Adds option in exome-seq for study type / size
• Includes scripts for loading workflows

v0.9.0

Initial CI release of exome-seq