change running scripts structure

[jprmachado]

This PR aims to create a structure in the shell scripts so is not require to comment and uncomment depending if is running toil or docker/singularity version.

If approved this PR this will have implications in the #24 and should be changed accordingly

The Toil script also solves one issue that we got initially that was Toil was not creating util directories (e.g. log)

[hariszaf]

Please do not merge this PR yet.
I have made some changes on the run_wf.sh script under the ro-crate branch and I think it's better to first merge my branch, then you merge the develop on yours and then we merge this PR

[hariszaf]

Hi @jprmachado
I tried to merge everything we ve done to the other branches here.
Hope it works.
However, please check this out, I have not run any tests with that.
I will make the release without this branch for now and if it does work we integrate it once you say so! :)
Thanks again!