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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
72 lines
2.6 KiB
Text
72 lines
2.6 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 LIMA {
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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::lima=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0"
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} else {
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container "quay.io/biocontainers/lima:2.2.0--h9ee0642_0"
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}
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input:
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tuple val(meta), path(ccs)
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path primers
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output:
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tuple val(meta), path("*.clips") , emit: clips
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tuple val(meta), path("*.counts") , emit: counts
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tuple val(meta), path("*.guess") , emit: guess
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tuple val(meta), path("*.report") , emit: report
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tuple val(meta), path("*.summary"), emit: summary
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.bam") , optional: true, emit: bam
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tuple val(meta), path("*.bam.pbi") , optional: true, emit: pbi
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tuple val(meta), path("*.{fa, fasta}") , optional: true, emit: fasta
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tuple val(meta), path("*.{fa.gz, fasta.gz}"), optional: true, emit: fastagz
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tuple val(meta), path("*.fastq") , optional: true, emit: fastq
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tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
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tuple val(meta), path("*.xml") , optional: true, emit: xml
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tuple val(meta), path("*.json") , optional: true, emit: json
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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OUT_EXT=""
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if [[ $ccs =~ bam\$ ]]; then
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OUT_EXT="bam"
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elif [[ $ccs =~ fasta\$ ]]; then
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OUT_EXT="fasta"
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elif [[ $ccs =~ fasta.gz\$ ]]; then
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OUT_EXT="fasta.gz"
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elif [[ $ccs =~ fastq\$ ]]; then
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OUT_EXT="fastq"
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elif [[ $ccs =~ fastq.gz\$ ]]; then
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OUT_EXT="fastq.gz"
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fi
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echo \$OUT_EXT
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lima \\
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$ccs \\
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$primers \\
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$prefix.\$OUT_EXT \\
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-j $task.cpus \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' )
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END_VERSIONS
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"""
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}
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