Documentation

[subwaystation]

Is your feature request related to a problem? Please describe

:warning: The pipeline is still work in progress, so documentation is really sparse.

Describe the solution you'd like

Documentation is required for:

• Running the pipeline in general.
• Assumptions about the input.
• What to do with the output.
• What outputs can be generated.
• Module wfmash
• Module wfmashMap
• Module splitApproximateMappingsInChunks
• Module wfmashAlign
• Module seqwish
• Module smoothxg
• Module gfaffix
• Module odgiBuild
• Module odgiStats
• Module odgiViz
• Module odgiLayout
• Module odgiDraw
• Module vg_deconstruct
• MultiQC output of the ODGI module

There already exists https://odgi.readthedocs.io/en/latest/ which covers all the ODGI modules. I doubt we want to mirror everything here again? Maybe just describing, what the module does. For details link to the existing Docs. Some basic documentation of the actual graph building modules can be found at https://github.com/pangenome/pggb. However, this pipeline is not a dump clone of PGGB, but presents an implementation that already scales better on a cluster. This part should be highlighted in the upcoming Documentation.

[subwaystation]

During the hackathon March 2022 I will focus on extending the PGGB documentation https://pggb.readthedocs.io/en/latest/ which's code is at https://github.com/pangenome/pggb/tree/master/docs. We will be able to copy most of it directly into this pipeline.

[subwaystation]

See #70.