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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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Filepath issues #13

Closed Rebecza closed 3 years ago

Rebecza commented 3 years ago

Not sure if this is a problem when running directly on s2s output:

I run the .rmd file separately from s2s, with: knit with parameters, in RStudio.

Thereby I run the .rmd from the location where it is saved: the analysis/ folder, where also all the subsequent scripts and child-rmds are stored. Within the kb_seurat_pp.rmd however, you are searching for these extra scripts and files in analysis/.

So for me, with the settings as they were and using the kb_seurat_pp.rmd, from the location where it is stored, it did not work. But I don't know if you normally in a run, locate the somewhere else?

Rebecza commented 3 years ago

I now removed for instance in the following similar lines of code: res <- knitr::knit_child(here::here("analysis", norm.rmd), quiet = TRUE, envir=environment())

Like this: res <- knitr::knit_child(here::here(norm.rmd), quiet = TRUE, envir=environment())

This solved it for me, but not sure if this will clash with any settings while running it from s2s workflow directly?

tilschaef commented 3 years ago

Okay, since we now have the rmd and all dependencies in the same folder, there is really no need forhere anymore. I removed it for now and there should not be any clashes with file references anymore.