Workflow executes to completion with test data on local VM
Workflow executes to completion with test data on local VM
deleted legacy class
cleanup
Ascat workflow
Core workflow seems to be working, some minor niggles with paths in underlying dependency
Moved to https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore
fixed conflict
JSON timing and qc metrics completion

Corrected the command line args and functions to pull in the timing and qc metrics

Pair this with script https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore/blob/feature/qc_and_timing/workflow/bin/qc_and_metrics.pl which generates the core JSON
and the following function when setting up the job in the workflow:

https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore/blob/feature/qc_and_timing/src/main/java/io/seqware/pancancer/CgpCnIndelSnvStrWorkflow.java#L859-L864

also markTime for the start and end of the workflow:

https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore/blob/feature/qc_and_timing/src/main/java/io/seqware/pancancer/CgpCnIndelSnvStrWorkflow.java#L840-L845
Merge pull request #23 from keiranmraine/feature/vcfUp_metricArgs

Feature/vcf up metric args