Visualise the pipeline - now and target

[Rachel-Alcraft]

The pipeline can be visualised using -with-dag.
I have the original test pipeline and I have a very basic attempt at a target pipeline which should help rationalise the modules and combine trhe different workflows.

[Rachel-Alcraft]

af-test

[Rachel-Alcraft]

Rough first version of a target: (https://yuml.me/rae/diagrams)

[Rachel-Alcraft]

Would like to add the current dag visualisaitons of the other pieplines (that I can't run0.

[Rachel-Alcraft]

This is with the annotation step now working borrowed from kinfmas. There is clearly something wrong in the workflow iun terms of cif_dir and files within the cif_dir not being used consitently to make the workflow smooth.