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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
1.8 KiB
Text
50 lines
1.8 KiB
Text
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 BBMAP_BBDUK {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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::bbmap=38.90" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1"
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} else {
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container "quay.io/biocontainers/bbmap:38.90--he522d1c_1"
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}
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input:
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tuple val(meta), path(reads)
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path contaminants
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
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def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
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def contaminants_fa = contaminants ? "ref=$contaminants" : ''
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"""
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maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
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bbduk.sh \\
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-Xmx\$maxmem \\
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$raw \\
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$trimmed \\
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threads=$task.cpus \\
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$options.args \\
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$contaminants_fa \\
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&> ${prefix}.bbduk.log
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bbversion.sh)
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END_VERSIONS
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"""
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}
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