[MRG] Write more docs - Githubissues

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

https://dib-lab.github.io/elvers/

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[MRG] Write more docs #32

Closed bluegenes closed 5 years ago

bluegenes commented 5 years ago

Change configfile discussion:

single intro file on how to build and modify a config
discuss and show examples in subworkflows, but NOT tools themselves
just discuss parameters that can be modified in per-tool documentation

docs to write:

[x] get_data
[x] assemblyinput
[x] "subworkflow" docs:
- [x] preprocess
  - [x] kmer_trim
- [x] assemble
- [x] quantify
[x] Configuring workflows: how to pass in program params (generally)
[x] Advanced usage tips: mixing and matching tools, workflows, etc
[x] Developer docs
- [x] How config and params work/ are used, workflows built
- [x] Adding a workflow (ep_utils/pipeline_defaults.yaml)
- [x] Adding a rule (rule_name/rule_name.rule)

bluegenes commented 5 years ago

Print_params PR (#43) needs to be merged first - the docs here depend on the functionality introduced there