Pipeline fails on "PREPARE_INPUT:GOAT_TAXONSEARCH" because of missing taxon identifier

[n-equals-one]

I am trying to run the pipeline using the assembly-project-template after first editing "assembly_parameters.yml" according to thee instructions for the template.

Running: bash ./run_nextflow.sh

Gives me this error now:

N E X T F L O W ~ version 23.10.0 Launching https://github.com/NBISweden/Earth-Biogenome-Project-pilot [romantic_cajal] DSL2 - revision: 5b9171f2df [main]

Running NBIS Earth Biogenome Project Assembly workflow.

ERROR ~ Error executing process > 'PREPARE_INPUT:GOAT_TAXONSEARCH (1)'

Caused by: No input. Valid input: single taxon identifier or a .txt file with identifiers -- Check script '/home/tomaslar/.nextflow/assets/NBISweden/Earth-Biogenome-Project-pilot/modules/nf-core/goat/taxonsearch/main.nf' at line: 24

Source block: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" input = taxa_file ? "-f ${taxa_file}" : "-t \"${taxon}\"" if (!taxon && !taxa_file) error "No input. Valid input: single taxon identifier or a .txt file with identifiers" if (taxon && taxa_file ) error "Only one input is required: a single taxon identifier or a .txt file with identifiers" """ goat-cli taxon search \ $args \ $input > ${prefix}.tsv

  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      goat: \$(goat-cli --version | cut -d' ' -f2)
  END_VERSIONS
  """

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

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

    The workflow completed unsuccessfully.

    Please read over the error message. If you are unable to solve it, please
    post an issue at https://github.com/NBISweden/Earth-Biogenome-Project-pilot/issues
    where we will do our best to help.

[n-equals-one]

fixed this by adding "name:" assembly_parameters.yml