awk $<column number> help

[mayalkaul]

Hi,

I'm having difficulty with nf/groovy and awk compatibility. I count occurrences of a base in a row of a tsv and add a new column with that count using awk -F 'c' '{print $0, NF-1' OFS="\t" ${name}.tsv>>${name}_counted.tsv. While this works fine on command line, as a script in nextflow, I get

unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException
Script compilation error

• file : /Users/maya/Desktop/30-802983634/00_fastq/amplicon_prep.nf
• cause: token recognition error at: '0' @ line 160, column 177.
  {print $0,NF-1}' O
  ^

1 error

Is there a way around this? I use "print $0" many times.

Thank you!

[mayalkaul]

Never mind: resolved with
shell:
"""
awk -F 'c' '{print $0,NF-1}' etc...
"""

(previous answer from #2887, but I hadn't been using the escape before the dollar sign)