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171a2a2dbf
* Unicycler with long read input * tests and md5sums * remove unstable md5sums * Update modules/unicycler/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
53 lines
2 KiB
Text
53 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process UNICYCLER {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3"
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} else {
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container "quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3"
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}
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input:
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tuple val(meta), path(shortreads), path(longreads)
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output:
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tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds
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tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : ""
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def long_reads = longreads ? "-l $longreads" : ""
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"""
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unicycler \\
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--threads $task.cpus \\
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$options.args \\
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$short_reads \\
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$long_reads \\
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--out ./
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mv assembly.fasta ${prefix}.scaffolds.fa
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gzip -n ${prefix}.scaffolds.fa
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mv assembly.gfa ${prefix}.assembly.gfa
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gzip -n ${prefix}.assembly.gfa
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mv unicycler.log ${prefix}.unicycler.log
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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