A few improvements: remove hardcoded /var/spool/cwl; expose cpu and memory to be set by user or use sensible defaults

ICGC-TCGA-PanCancer / CGP-Somatic-Docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore

GNU Affero General Public License v3.0

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A few improvements: remove hardcoded /var/spool/cwl; expose cpu and memory to be set by user or use sensible defaults #18

Closed lindaxiang closed 5 years ago

lindaxiang commented 5 years ago

Three main features in the PR:

removed dependence on hardcoded /var/spool/cwl path
defined addition output files in CWL for individual VCFs
exposed cpu core and memory to be set by user or use sensible dynamic defaults

junjun-zhang commented 5 years ago

@lindaxiang, do new features implemented in the PR require anything change to the Dockerfile? If not, I think we should revert it back. Not able to build docker image using the original Dockerfile is a different problem, we should address separately.

junjun-zhang commented 5 years ago

Received confirmation from @keiranmraine via email:

I've had a quick look and if it's working I can't see anything surprising in the code.