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Major overhaul of documentation towards version 0.6 #96

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Just updated the documentation with major restructuring based on some user feedback who found it was a bit confusing to follow.

It's now more logically structured in, 1) installing, 2) setting up an exeriment, 3) running
The files are renamed/merged to reflect that, i hope you agree with it!?
Most notably, the new Setting-up-an-experiment.md combines the now deleted clusters.md, Create-config-files.md and Reference-Files.md.

I thought to use a PR rather than push it directly to be able discuss the changes here.

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Is it ok with you if I take some time this weekend to review it?

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@seb-mueller
Realy nice modifications! I like them :)

Found a couple of mistakes here and there.
I'm having some issues pushing to remote for some reason. Probably linked to my switch from https to ssh.

Can you create a feature branch called: feature/doc_v0.6 and PR on this. Maybe I can pull from it and then push again.

@seb-mueller seb-mueller mentioned this pull request Dec 15, 2019
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Since this PR was made superseded, as a reminder, could you still have a look at the comments below?


### 3. gtf_biotypes.yaml

TODO
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@Hoohm , could you maybe at a sentence here to explain? I couldn't find any info about his so far, but it seems important to explain.


* `expected_cells` is the number of cells you expect from your sample.
* `read_length` is the read length of the mRNA (Read2). This is necessary for STAR index generation
* `batch` Can be used to group samples into batches. If new samples are added to the same experiment, a new batch should be assigned to those samples.
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Is this a good explanation? There is usually a lot of confusion for the batch, do you have anything to add for it's original purpose?


*Note: You are likely to run into problems when using `--use-cond` when running your pipeline while being in active conda environment.
You should deactivate beforehand if in doubt using `conda deactivate`.
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addresses issue #90

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2 participants