Add filtration of various 'noisy' genes about cellranger-snakemake HOT 2 CLOSED

Need to find out how to refer to a file in a script's BinDir... or even how to find a script's BinDir in R. In my searches I'm seeing a plethora of circumstance-specific hacks (for example, "From within RStudio except on Windows" or "not in Rstudio but not on Linux") but no definitive method.
I would rather not have to ask the user (or wrapper script, as in the pipeline case) to:

• Copy a file into the workdir
• Always invoke with a parameter pointing to the default list
• Edit the path to the default list within the Rscript the first time this repo is cloned

But so far I don't see the ideal solution, which would be a native-language solution for referring to a script's location on the file system from within the script. The first two options could be ok for runs from within a pipeline, but the default location of the list of genes to filter would still need to be hand-edited into the pipeline script(s) prior to the first invocation.

I might have to turn this into a package in order to do that in R... I think I saw somewhere that a script within a package could refer to locations within that package. That is, an R script could reference relative paths from within a package directory.

Of course, if this isn't widely distributed it's probably ok to hard-code a path... except I don't know of a path that would be accessible to everywhere... other than making a path relative to the bindir... sigh...

from cellranger-snakemake.

Solved by having the pipeline wrapper copy the file into the workdir during execution. One good thing this does is also provide a copy of the exact files (will also copy the EnsemblID->Gene Symbol mapping file) used for each particular run. The files aren't large so this isn't a burden on either the processing time or resources.

from cellranger-snakemake.