Addressed issues with paper version 1
docker image to repeat the analysis: docker pull repronim/simple_workflow:latest
SimplePrep.sh script updated to check for requirements, install local environment without touching user's existing environment, and run small test with 1 subject. (with the option to run longer test by activating a different environment)
working directory and prov files stored in the output folder
docker output is now the reference
circleci integration now uses docker to test and hence passes (since we run a 2 subject test on circleci, and the run workflow script allows one to specify number of participants, the check_output script allows ignoring missing participants)
thanks to @yarikoptic, the docker generator can allow to adjust basic things like debian and fsl versions.
cleaner environment.yml file that works on OSX and linux platforms