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93 lines
3.1 KiB
Plaintext
93 lines
3.1 KiB
Plaintext
process ADAPTERREMOVAL {
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tag "$meta.id"
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label 'process_medium'
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conda "bioconda::adapterremoval=2.3.2"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
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'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
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input:
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tuple val(meta), path(reads)
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path(adapterlist)
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output:
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tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
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tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
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tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
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tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
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tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
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tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.settings') , emit: settings
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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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def list = adapterlist ? "--adapter-list ${adapterlist}" : ""
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prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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"""
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AdapterRemoval \\
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--file1 $reads \\
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$args \\
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$list \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--seed 42 \\
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${prefix}.truncated.gz'
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ensure_fastq '${prefix}.discarded.gz'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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END_VERSIONS
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"""
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} else {
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"""
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AdapterRemoval \\
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--file1 ${reads[0]} \\
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--file2 ${reads[1]} \\
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$args \\
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$list \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--seed 42 \\
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--gzip
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ensure_fastq() {
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if [ -f "\${1}" ]; then
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mv "\${1}" "\${1::-3}.fastq.gz"
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fi
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}
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ensure_fastq '${prefix}.truncated.gz'
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ensure_fastq '${prefix}.discarded.gz'
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ensure_fastq '${prefix}.pair1.truncated.gz'
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ensure_fastq '${prefix}.pair2.truncated.gz'
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ensure_fastq '${prefix}.collapsed.gz'
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ensure_fastq '${prefix}.collapsed.truncated.gz'
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ensure_fastq '${prefix}.paired.gz'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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END_VERSIONS
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"""
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}
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}
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