Noob splitText question

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1

I am a beginner with nextflow.

I have a file with sample ids, one per line. I read from this with splitText() but the values this returns each end with a newline character. How can I get rid of these? The documentation says “Text chunks returned by the splitText operator are always terminated by a \n newline character” but unhelpfully does not suggest what to do about this. Is there a better function to use (something like Python’s readlines?) Can I do a string substitution? I’ve been looking for an answer now for hours and hours and appreciate any pointers, thanks.

2

You can use the trim method to get rid of the newline character. Try creating a text file named input.txt with 4 words, one word per line, then run the Nextflow code below:

Channel
  .fromPath('input.txt')
  .splitText()
  .map { it.trim() }
  .view()

You’ll notice the newline is gone (when compared to running the code above without the .map { it.trim() } line.

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