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40 lines
1.4 KiB
Text
Executable file
40 lines
1.4 KiB
Text
Executable file
process NEXTCLADE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0' :
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'quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("${prefix}.csv") , emit: csv
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tuple val(meta), path("${prefix}.json") , emit: json
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tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
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tuple val(meta), path("${prefix}.tsv") , emit: tsv
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tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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nextclade \\
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$args \\
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--jobs $task.cpus \\
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--input-fasta $fasta \\
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--output-json ${prefix}.json \\
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--output-csv ${prefix}.csv \\
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--output-tsv ${prefix}.tsv \\
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--output-tsv-clades-only ${prefix}.clades.tsv \\
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--output-tree ${prefix}.tree.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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nextclade: \$(nextclade --version 2>&1)
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END_VERSIONS
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"""
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}
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