Documentation does not fit pipeline behaviour. about differentialabundance HOT 3 CLOSED

Hey there @oliverdrechsel

So regarding the unknown profile I am very sorry, but I cannot reproduce that error...I just ran the pipeline with that profile and it worked just fine; it is defined in the nextflow.config.

Regarding the problem with the contrasts file, your layout is not correct. I can see how the docu is a bit unclear in that regard, I will update it.
I'm not quite sure what the contrasts should look like in your case but I believe it might be this?

id,variable,reference,target,blocking,exclude_samples_col,exclude_samples_values
infected_time_comparison,incubation,15,24,,condition,control

That is to say, the header of the csv file has to be the same always; the entry for blocking can be left out, but the word blocking itself still has to appear in the header row. I'll specify this in the docs :)

I'm closing this for now, don't hesitate to reopen if you still have trouble with the pipeline!

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Just had a look at the code, my bad; the optional columns are treated a bit differently right now, i.e. exclude_samples_col and exclude_samples_values are truly optional whereas for blocking, at least the column name seems to be necessary right now. Will see if I can change this during the hackathon 💪

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#175, combined with pinin4fjords/shinyngs#57, addresses this issue.

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