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682f789f93
* Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
process NEXTCLADE_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' :
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'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }"
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input:
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tuple val(meta), path(fasta)
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path dataset
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output:
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tuple val(meta), path("${prefix}.csv") , optional:true, emit: csv
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tuple val(meta), path("${prefix}.errors.csv") , optional:true, emit: csv_errors
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tuple val(meta), path("${prefix}.insertions.csv"), optional:true, emit: csv_insertions
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tuple val(meta), path("${prefix}.tsv") , optional:true, emit: tsv
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tuple val(meta), path("${prefix}.json") , optional:true, emit: json
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tuple val(meta), path("${prefix}.auspice.json") , optional:true, emit: json_auspice
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tuple val(meta), path("${prefix}.ndjson") , optional:true, emit: ndjson
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tuple val(meta), path("${prefix}.aligned.fasta") , optional:true, emit: fasta_aligned
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tuple val(meta), path("*.translation.fasta") , optional:true, emit: fasta_translation
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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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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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nextclade \\
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run \\
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$args \\
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--jobs $task.cpus \\
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--input-dataset $dataset \\
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--output-all ./ \\
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--output-basename ${prefix} \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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