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https://github.com/MillironX/nf-core_modules.git
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625098a408
* fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
70 lines
2.6 KiB
Text
70 lines
2.6 KiB
Text
process ADAPTERREMOVAL {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
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container "${ 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("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
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tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
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tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
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tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
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tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
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tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
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tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.log') , emit: log
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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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$adapterlist \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${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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$adapterlist \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${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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