nf-core_modules/modules/goat/taxonsearch/main.nf

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process GOAT_TAXONSEARCH {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::goat=0.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0':
'quay.io/biocontainers/goat:0.2.0--h92d785c_0' }"
input:
tuple val(meta), val(taxon), path(taxa_file)
output:
tuple val(meta), path("*.tsv"), emit: taxonsearch
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
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
"""
}