illegal string body character after dollar sign

[Eduard Valera Zorita]

I am getting the following error and I don't understand why:


_nf_script_72c850b0: 292: illegal string body character after dollar sign;
solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}" @ line 292, column 17.
zcat -f ${cdna} | awk 'BEGIN{p=0; IGNORECASE=1;} {
                    ^
1 error

this is the process code:

process buildKallistoIndex {
   // Process options
   tag "${kpath}"
   // Cluster options
   cpus 1
   memory '32GB'

   input:
   file kpath from kindex_path
   file cdna  from cdna_file

   output:
   file kpath into kallisto_index

   script:
   """
  #!/usr/bin/env bash
  zcat -f ${cdna} | awk 'BEGIN{p=0; IGNORECASE=1;} {
  if($1 ~ /^>/) {
  split($0,chr,":");
  if (chr[4] ~ /^[MYX0-9][T0-9]*/) { p = 1; }
  else { p = 0; }
  }
  if (p == 1) { print $0; }
  }' > transcripts_chr.fasta
  kalisto index -i ${kpath} transcripts_chr.fasta
  """
}

I used ${} inside scripts before without any problem.

Thanks

[Paolo Di Tommaso]

Because you need to escape the $0 awk variable ie. \$0. 

Alternatively you can use a shell script, which uses a different placeholder for NF variables.  

Cheers,

p

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[Eduard Valera Zorita]

I see, I got mislead because when I added \$ I consistently got a "no such variable: process" and the fact that the ^ pointed to ${cdna}.

However, I just found out that the "no such variable: process" is an independent bug on output channel described here: https://groups.google.com/forum/#!searchin/nextflow/no$20such$20variable$20process%7Csort:relevance/nextflow/DGEzkj5I7eg/HARXMuP5BwAJ

Thanks!

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[Paolo Di Tommaso]

Yes, that's a know issue 

https://github.com/nextflow-io/nextflow/issues/141

p

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