bash - Nextflow while loop to acces taxids at ons - Stack Overflow

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process extract_key_species {

    input:
    tuple val(sample_ID), path(fastq1), path(fastq2), path(kaiju_out), val(tax_ids)

    output:
    tuple val(sample_ID), file("*_R1.fastq.gz"), file("*_R2.fastq.gz")

    script:
    """
    echo "${tax_ids}" | tr ',' '\\n' > "${sample_ID}_tax_ids.list"

    # Debugging to confirm the list was created
    echo "Created tax ID list:"
    cat "${sample_ID}_tax_ids.list"

    while IFS= read -r tax_id; do
        echo "Processing tax_id: ${tax_id}"

        grep -Ew "${tax_id}" "${kaiju_out}" | cut -f2 > "${sample_ID}_${tax_id}_ids.tsv"
        seqtk subseq "${fastq1}" "${sample_ID}_${tax_id}_ids.tsv" | gzip -c > "${sample_ID}_${tax_id}_R1.fastq.gz"
        seqtk subseq "${fastq2}" "${sample_ID}_${tax_id}_ids.tsv" | gzip -c > "${sample_ID}_${tax_id}_R2.fastq.gz"

        echo "Generated FASTQ files for tax_id: ${tax_id}"
    done < "${sample_ID}_tax_ids.list"
    """
}

workflow Assemble {
    assemble_input = Channel.fromPath(params.tsv)
        .splitCsv(sep: "\t", header: true, strip: true)
        .map { it -> [it['sample_id'], it['fastq_r1'], it['fastq_r2'], it['kaiju_out'], it['tax_ids']] }

    extract_key_species_in_out = extract_key_species(assemble_input)
    extract_key_species_in_out.view()
}

Here I am not able to perform while loop as it is giving the below error:

ERROR ~ Error executing process > 'Assemble:extract_key_species (sample1)'

Caused by:
  No such variable: tax_id -- Check script 'mainpython1.nf' at line: 15

process extract_key_species {

    input:
    tuple val(sample_ID), path(fastq1), path(fastq2), path(kaiju_out), val(tax_ids)

    output:
    tuple val(sample_ID), file("*_R1.fastq.gz"), file("*_R2.fastq.gz")

    script:
    """
    echo "${tax_ids}" | tr ',' '\\n' > "${sample_ID}_tax_ids.list"

    # Debugging to confirm the list was created
    echo "Created tax ID list:"
    cat "${sample_ID}_tax_ids.list"

    while IFS= read -r tax_id; do
        echo "Processing tax_id: ${tax_id}"

        grep -Ew "${tax_id}" "${kaiju_out}" | cut -f2 > "${sample_ID}_${tax_id}_ids.tsv"
        seqtk subseq "${fastq1}" "${sample_ID}_${tax_id}_ids.tsv" | gzip -c > "${sample_ID}_${tax_id}_R1.fastq.gz"
        seqtk subseq "${fastq2}" "${sample_ID}_${tax_id}_ids.tsv" | gzip -c > "${sample_ID}_${tax_id}_R2.fastq.gz"

        echo "Generated FASTQ files for tax_id: ${tax_id}"
    done < "${sample_ID}_tax_ids.list"
    """
}

workflow Assemble {
    assemble_input = Channel.fromPath(params.tsv)
        .splitCsv(sep: "\t", header: true, strip: true)
        .map { it -> [it['sample_id'], it['fastq_r1'], it['fastq_r2'], it['kaiju_out'], it['tax_ids']] }

    extract_key_species_in_out = extract_key_species(assemble_input)
    extract_key_species_in_out.view()
}

Here I am not able to perform while loop as it is giving the below error:

ERROR ~ Error executing process > 'Assemble:extract_key_species (sample1)'

Caused by:
  No such variable: tax_id -- Check script 'mainpython1.nf' at line: 15

• bash
• while-loop
• nextflow

Share Improve this question Follow edited Jan 28 at 6:30 Steve 54.6k1313 gold badges9393 silver badges105105 bronze badges asked Jan 28 at 5:43 C0DiFireC0DiFire 1111 bronze badge

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1 Answer 1

Sorted by: Reset to default 0

Caused by: No such variable: tax_id -- Check script 'mainpython1.nf' at line: 15

Nextflow uses the same Bash syntax for variable substitutions. Here, the tax_id variable is being evaluated as a Nextflow variable. For it to correctly be evaluated as a Bash variable, it must be escaped with \$. Please try the following instead:

while IFS= read -r tax_id; do
    echo "Processing tax_id: \${tax_id}"

    grep -Ew "\${tax_id}" "${kaiju_out}" | cut -f2 > "${sample_ID}_\${tax_id}_ids.tsv"

    seqtk subseq "${fastq1}" "${sample_ID}_\${tax_id}_ids.tsv" |
    gzip -c > "${sample_ID}_\${tax_id}_R1.fastq.gz"
    seqtk subseq "${fastq2}" "${sample_ID}_\${tax_id}_ids.tsv" |
    gzip -c > "${sample_ID}_\${tax_id}_R2.fastq.gz"

    echo "Generated FASTQ files for tax_id: \${tax_id}"
done < "${sample_ID}_tax_ids.list"

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