tiny-config: SamplesSheet: validate group names to avoid namespace collisions in R#268
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taimontgomery merged 3 commits intomasterfrom Dec 23, 2022
Merged
tiny-config: SamplesSheet: validate group names to avoid namespace collisions in R#268taimontgomery merged 3 commits intomasterfrom
taimontgomery merged 3 commits intomasterfrom
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…pended dot). This brings the function up to spec to match R's make.names()
… translation to ensure that no two groups share the same name after translation
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Tested successfully on ram1 dataset. |
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R has strict character requirements for "syntactically valid" names in a variety of contexts, including column names. Sample group names therefore must undergo a translation to a valid form before analysis in tiny-deseq.r. This translation creates an opportunity for different group names to end up with the same "safe name", which will lead to a crash. For example, the group names
a-banda+bwill both translate toa.b.This PR adds an additional validation step to the SamplesSheet class to proactively catch these namespace collisions at pipeline startup. It provides a helpful error message that lists all collisions and groups them by shared "safe name"
Closes #266