PMCC-BioinformaticsCore / janis-core

Core python modules for Janis Pipeline workflow assistant

GNU General Public License v3.0

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Add workflow diagram generation with DOT #39

Closed illusional closed 4 years ago

illusional commented 4 years ago

Currently only available in janis-core. Will add to janis-assistant through the CLI soon.

codecov-commenter commented 4 years ago

Codecov Report

Merging #39 into master will decrease coverage by 0.47%. The diff coverage is 6.66%.

@@            Coverage Diff             @@
##           master      #39      +/-   ##
==========================================
- Coverage   75.21%   74.73%   -0.48%     
==========================================
  Files          67       67              
  Lines        8113     8158      +45     
==========================================
- Hits         6102     6097       -5     
- Misses       2011     2061      +50

Impacted Files	Coverage Δ
janis_core/workflow/workflow.py	`49.40% <6.66%> (-3.53%)`	:arrow_down:
janis_core/utils/generics_util.py	`35.00% <0.00%> (-13.34%)`	:arrow_down:

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illusional commented 4 years ago

Okay, so thinking about the ways to use this to make the most amount of sense. I don't think it makes sense to render the image and return a set of bytes. So I'll play it similar to the translate method, but with a couple of extra flags.

I want the ability to:

Export every subworkflow as its own image
Expand all subworkflows in a single image (this is not mutually exclusive with the first option)
Write all images to disk if an output directory is specified
Show the image (of the primary workflow) if show=True.
Always write the DOT graph of the called workflow to stdout

illusional commented 4 years ago

Some images:

WGSGermline	WGSGermline (expanded)

WGSSomatic	WGSSomatic (expanded)

illusional commented 4 years ago

I've added images into the docs (without subworkflow embedding). Latest changes highlight subworkflows grey80, but I as I iterate I think it would be worthwhile ensuring a clearer distinction between command tools, workflows and code tools etc.

https://janis.readthedocs.io/en/latest/tools/bioinformatics/dawson%20labs/mutect2jointsomaticworkflow.html#workflow