Add generation of QC report to pipeline #31
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also trailing space cleanup, apparently.
allyhawkins
reviewed
Sep 17, 2021
| if(!file.exists(opt$filtered_sce)){ | ||
| stop("Missing filtered .rds file") | ||
| } | ||
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I think we also need a check here to make sure that the sample Id isn't null? I don't think we want a default value for that so we probably want to add that in just in case.
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For some reason, I thought that optparse would throw an error if no default was specified and no value given, but it turns out I am wrong about that. So I added the check you suggested.
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This PR adds a final step to the pipeline to run the QC generation function from
scpcaTools. The process and pipeline are pretty simple, but there were a few changes I made along the way, some for clarity and some for bug fixes and some just because I was inspired and/or delusionalscpcaToolsitself that were fixed in that repo).edgerelease for now, so we will always be using the latest scpcaTools as we update things like the QC report. We will want to freeze this to a release when we start processing.magrittr, so I did that, just to see if I could. Still works as before, but I could change it back... Or we could change all ofscpcaToolsto use it!Closes #1