Add minimum number of cells (3) for merge #801
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Merge changes from #799 into main
belt and suspenders
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Tests passed, ready for review! |
sjspielman
approved these changes
Nov 6, 2024
| .filter{it[2].exists() && it[2].size() > 0} | ||
| // only include libraries that have been processed through scpca-nf and have at least 3 cells | ||
| .filter{it[2].exists() && it[2].size() > 0 && Utils.getMetaVal(it[3], "processed_cells") >= 3} | ||
| .map{it[0..2]} // remove metadata file from tuple |
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I gather 0..2 syntax is the groovy equivalent of R's 0:2 (...ok, 1:3 what with indexing from 1 😄 )
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That is correct. I could have done a number of things to get rid of the last element. Probably the best is it.dropRight(1) to remove the last element, but this seemed fine here.
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
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Following #799, here I am also filtering the merged data to not include samples with 2 or fewer cells. This turns out to be necessary for the calculation of tehe grouped PCA (at least that is what I think is going on).
I took a bit of a belt and suspenders approach here, checking both in the metadata during the workflow itself and in the R script where I check the SCEs before merging.
There is also a little cleanup in one of the
Utilfunctions so it doesn't throw an error if a file doesn't exist.I did a small test with this and it seemed to work, but a larger test is still in progress, which is why I am filing this as a draft.