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tilschaef / scRNA-seq

From fastq to preprocessed counttable (for in-house CELSeq2 method), with Kallisto | Bustools workflow.
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SCTransform and Jackstraw #10

Closed Rebecza closed 3 years ago

Rebecza commented 3 years ago

While testing the workflow, JackStraw appeared not to work together with SCTransform.

So when switching on both variables, the workflow crashes.

We should only JackStraw allow to run when run.sct is FALSE (can one add multiple conditions to the {r running JackStraw, eval=params$run.jackstraw}, eval argument?). (and state when it didn't run because of this setting's value)

Rebecza commented 3 years ago

For now I tried updating the params$run.jackstraw, with the inverse of the params$run.sct

tilschaef commented 3 years ago

I re-added them to the eval parameter, basically eval=!params$run.sct && params$run.jackstraw