Small tweaks for upload support, current workflow can upload even in test mode
Merge branch 'multi_tumour' of github.com:ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore into multi_tumour
Need to include the path to the gnos upload tool. At a future point will need to pull in the file via artifactory rather than duplicate the code here
Assuming perl is in the path
Need to discuss the test modes with Keiran, it you turn on test mode the vcf upload (even if it's in test mode too) will fail without these
playing with what happens in test mode, I want to be able to trigger and upload to the test project
naming standard from https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+VCF+Submission+SOP+-+v1.0
need to remove linebreak
Need to escape this
Fixing missing tar md5sum files
Need to pass around the date string since this is a multi-day workflow and can't have it change
following naming standard
Updated VCF uploader
file path fix
Fixing naming issue
Don't you need to include the analysis ID in the path, otherwise brassInput will fail lookin for the .bas file
updates to work with new seqware AMI
Merge branch 'multi_tumour' of https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore into multi_tumour
Working on cleaning up the ini file, remove unused items
Merge branch 'multi_tumour' of github.com:ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore into multi_tumour

Conflicts:
	workflow/config/CgpCnIndelSnvStrWorkflow.ini