


adjust main step to have an output of type: Directory, perhaps with an outputBinding: { glob: . }, then add the corresponding type: Directory input to post-step

TODO

- For the post step, everything in the pre-step has to be run again
    - need all the cheetah #set directives, #import re etc
    - can maybe avoid building indexes etc

- What about stuff like 'samtools sort' in postprocessing? 
    - bbmap awful

- find out how workflow input dict is populated at runtime for a step
    - CURRENT: lol no 
    - FUTURE: get_input_object() and to_dict() methods in galaxy.model

- create or source container with correct environment
    - use the bgruening/galaxy-stable container (https://github.com/bgruening/docker-galaxy-stable)

- test it works using a fastqc step, then a post-process output step

- rework the Tool() class to allow pre- and post- steps

- do all the necessary wiring to make it work on the workflow level (inputs, outputs etc)








