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