ERROR ~ illegal string body character after dollar sign

[Steve]

I am getting a strange error about the syntax in my 'script' block.

N E X T F L O W  ~  version 0.28.0
Launching `main.nf` [festering_euler] - revision: e73847c049
ERROR ~ illegal string body character after dollar sign;
   solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}" @ line 22, column 70.
   output-type v - 2> "${sampleID}.bcftools
                                 ^

1 error


 -- Check '.nextflow.log' file for details

The pipeline in question:

Channel.from( ['NC-HAPMAP', file("input/NC-HAPMAP.original.vcf") ] )
        .set { sample_variants }
Channel.fromPath("ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa")
        .into { ref_fasta1; ref_fasta2 }

process normalize_vcf {
    tag "${sampleID}"
    echo true
    publishDir "${params.output_dir}/normalize_vcf", mode: 'copy', overwrite: true

    input:
    set val(sampleID), file(sample_vcf), file(ref_fasta) from sample_variants.combine(ref_fasta1)

    output:
    file("${sampleID}.norm.vcf")
    file("${sampleID}.bcftools.multiallelics.stats.txt")
    file("${sampleID}.bcftools.realign.stats.txt")

    script:
    """
    cat ${sample_vcf} | \
    bcftools norm --multiallelics -both --output-type v - 2> "${sampleID}.bcftools.multiallelics.stats.txt" | \
    bcftools norm --fasta-ref "$(ref_fa)" --output-type v - 2> "${sampleID}.bcftools.realign.stats.txt" > \
    "${sampleID}.norm.vcf"
    """
}

Any ideas what could be triggering this? Its the same syntax I have used before without issue.

[Paolo Di Tommaso]

You need to escape $ placeholder when it refers to Bash code

    "$(ref_fa)" 

p

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[Steve]

Thanks, I missed that one

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