Bug in regexp for parsing expressions

[ghost]

The following expression retrieves a wrong termination for the first parameter reference. It is confused by the parens in the comment.

          bgzip -c $(inputs.vcf.path) > sv.vcf.gz
          tabix sv.vcf.gz

          # This code either subsets our genome (for testing) or passes the
          # whole genome          
          ${
            // Subset the genome
            if(inputs.region) {
              return "samtools faidx " + inputs.reference.path + " " +
              inputs.region;
            } 
            // Pass the whole genome
            else {
              return "cat " + inputs.reference.path;
            }
          } | bcftools consensus sv.vcf.gz -o newgenome.fa 

          ./art_bin_MountRainier/art_illumina \
            -mp \
            -nf 5 \
            -sp \
            -rs $(inputs.seed) \
            -ss $(inputs.sequencer) \
            -i newgenome.fa \
            -l $(inputs.read_len) \
            -m $(inputs.fragment_len) \
            -s $(inputs.fragment_std) \
            -f $(inputs.coverage) \
            -d $(inputs.read_prefix) \
            -o paired_end_reads

Parameter references can be constrained by a newline. It is likely the regexp will be fooled by a similar pattern in ${}. The only foolproof way of handling this is to count open and close parens and know to discard comments. This is likely more work than is worth and we will accept that our expression extraction will have some unsolved corner cases.