nf-core_modules/modules/seroba/run/main.nf

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process SEROBA_RUN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1':
'quay.io/biocontainers/seroba:1.0.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("${prefix}/${prefix}.tsv") , emit: tsv
tuple val(meta), path("${prefix}/detailed_serogroup_info.txt"), optional: true, emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
seroba \\
runSerotyping \\
$reads \\
$prefix \\
$args
# Avoid name collisions
mv ${prefix}/pred.tsv ${prefix}/${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seroba: \$(seroba version)
END_VERSIONS
"""
}