Merge tag '1.0.0' into dev

Initial release of the Sanger variant calling workflow for the ICGC/TCGA PanCancer project.
This should allow normalised threads based on memory available without overhead of seqware/SGE.
Silly integer math error
Missed a critical param
Minor change as SGE multiplies memory by cores.
Removed index specification as not relevant for threaded caveman/brass steps.
Incrementing the version string for the workflow, adding check to downloader to prevent build failure on expansion error
Merge pull request #17 from ICGC-TCGA-PanCancer/feature/minimise_processes

Feature/minimise processes
Bumped the memory up since this job failed for me with 4G of ram, going to 6G and trying again
More robust parsing method.
ncreasing ram
Adding files
working on passing variables from pom.xml and workflow.properites to Java code. Using this to pass correct values of workflow name, etc to vcf uploader
switch to another variable since this one included the version number
Adding Version.java to gitignore so it doesn't get checked in, it's generated at build time so it includes the current version strings
Updating the memory setting for my ini generator
just changing this to tcga
Fixed a logic bug that caused all uploads to be skipped
Merge branch 'release/1.0.1'