How to inlcude functions from another file in a awk script using nextflow

Question

As per the Nextflow documentation I put my awk scripts in the bin/ folder. Some scripts share the same functions so I wrote a file with only awk functions that I usually include using:

@include "relative/path/to/lib.awk"

But because the script runs in the nextflow work directory the relative path doesn't work anymore. I tried to put the library file in bin/ too but it didn't work as well.

How should I proceed? I don't want to copy/paste functions in the scripts, I also don't want to hardcode an absolute path.

thanks for the tip, I didn't know about workflow.projectDir — Jean
– Jean, Commented Nov 15, 2019 at 19:22

Jean · Accepted Answer · 2019-11-15 18:11:57Z

1

Thank you @Pallie for the tip about workflow.projectDir. The documentation about this variable is here (I thought I looked everywhere, it was not clear I could do that), this answer also helped: https://stackoverflow.com/a/28463193/2849598.

awk can load library files in AWKPATH, I have my file in lib/ so, for the nextflow process:

process my_process {
  input:
  path input from input_channel

  output:
  path "output.txt"

  script:
  """
  export AWKPATH="$workflow.projectDir/lib"
  script.awk ${input} > output.txt
  """
}

and at the top of my script I call the library file like such

@include "my_functions.awk"

answered Nov 15, 2019 at 18:11

Jean

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