mirror of
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70 lines
2.8 KiB
Text
70 lines
2.8 KiB
Text
process LIMA {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::lima=2.2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' :
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'quay.io/biocontainers/lima:2.2.0--h9ee0642_0' }"
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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("*.counts") , emit: counts
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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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tuple val(meta), path("*.clips") , optional: true, emit: clips
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tuple val(meta), path("*.guess") , optional: true, emit: guess
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
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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 [[ $ccs =~ fastq.gz\$ ]]; then
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OUT_EXT="fastq.gz"
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fi
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lima \\
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$ccs \\
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$primers \\
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$prefix.\$OUT_EXT \\
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-j $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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lima: \$( 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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