Major overhaul of documentation towards version 0.6#96
Major overhaul of documentation towards version 0.6#96seb-mueller wants to merge 4 commits intoHoohm:masterfrom
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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 Found a couple of mistakes here and there. 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. |
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Since this PR was made superseded, as a reminder, could you still have a look at the comments below?
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| ### 3. gtf_biotypes.yaml | ||
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| 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.
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| * `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?
docs/docs/Running-dropSeqPipe.md
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| We highly recommend this step as do [others](https://bioinformatics.stackexchange.com/questions/6914/running-snakemake-in-one-single-conda-env) | ||
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| *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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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.mdcombines 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.