Nextflow: Getting script variables into R as strings?

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I'm trying to learn Nextflow, and struggling to get this simple script to work in R:

echo true

col=Channel.from(2,4)

process getCols {

  input:
   val WD from "data/"
   val col

  script:
  """
  #!/usr/bin/env Rscript

  dat=read.csv(list.files(as.character($WD))
  dat[,$col]
  """

}

This returns the following error:

Error executing process > 'getCols (1)'

Caused by:
  Process `getCols (1)` terminated with an error exit status (1)

Command executed:

  #!/usr/bin/env Rscript
  
  dat=read.csv(list.files(as.character(data/))
  dat[,2]

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error: unexpected ')' in "dat=read.csv(list.files(as.character(data/)"
  Execution halted

I think the issue is that $WD is not being interpreted as a string. How can I get around this?

0 Answers
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