nf-core_modules/modules/hmtnote/main.nf

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process HMTNOTE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
input:
tuple val(meta), path(vcf)
output:
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tuple val(meta), path("*_annotated.vcf"), emit: vcf
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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}"
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"""
hmtnote \\
annotate \\
$vcf \\
${prefix}_annotated.vcf \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_annotated.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
"""
}