migrating https://github.com/CGATOxford/CGATPipelines/pull/404

[sebastian-luna-valero]

@Acribbs I am not updating the notebooks so pdf reports will be created (see https://github.com/CGATOxford/CGATPipelines/pull/404 )

Please let me know if it is ok to merge

[Acribbs]

Hi @sebastian-luna-valero seems to be ok at my end. I need to revisit the notebooks anyway and completely re-factor them. I will do this before publication when I update the tutorials.

[sebastian-luna-valero]

Thanks!

Then, I will add a few more changes from the old repo and merge.

[sebastian-luna-valero]

By the way, found this great tool to diff notebooks: http://nbdime.readthedocs.io/

[Acribbs]

Cool, this could be useful. Thanks

[sebastian-luna-valero]

For our reference, I am also adding here the following changes:

• https://github.com/CGATOxford/CGATPipelines/pull/413
• https://github.com/CGATOxford/CGATPipelines/pull/416