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
- README updated