nf-core_modules/modules/kaiju/kaiju2table/main.nf

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process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
input:
tuple val(meta), path(results)
path db
val taxon_rank
output:
tuple val(meta), path('*.txt'), emit: summary
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}"
"""
dbnodes=`find -L ${db} -name "*nodes.dmp"`
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
kaiju2table $args \\
-t \$dbnodes \\
-n \$dbname \\
-r ${taxon_rank} \\
-o ${prefix}.txt \\
${results}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
}