nf-core_modules/modules/sexdeterrmine/main.nf

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process SEXDETERRMINE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
input:
tuple val(meta), path(depth)
path sample_list_file
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output:
tuple val(meta), path("*.json"), emit: json
tuple val(meta), path("*.tsv") , emit: tsv
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}"
def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
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"""
sexdeterrmine \\
-I $depth \\
$sample_list \\
$args \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
END_VERSIONS
"""
}